diff --git a/config.toml b/config.toml
index 22ac65175a1dacb87dcc43223cb2420c2ea08d78..4acf35bf27ece8e8748ff06b7b76b8692ff73c0c 100644
--- a/config.toml
+++ b/config.toml
@@ -49,12 +49,12 @@ paginate = 10
weight = 3
identifier = "publications"
url = "/publications/"
-# [[menu.main]]
-# name = "Biorepository"
-# pre = "<i class='fas fa-stethoscope fa-fw'></i>"
-# weight = 4
-# identifier = "repository"
-# url = "/repository/"
+ [[menu.main]]
+ name = "Biorepository"
+ pre = "<i class='fas fa-stethoscope fa-fw'></i>"
+ weight = 4
+ identifier = "repository"
+ url = "/repository/"
[[menu.main]]
name = "Single-Cell Data"
pre = "<i class='fas fa-chart-bar fa-fw'></i>"
diff --git a/data/repository/filters.json b/data/repository/filters.json
new file mode 100644
index 0000000000000000000000000000000000000000..633c958ee781bb83860c30e2bd984929e2f886f1
--- /dev/null
+++ b/data/repository/filters.json
@@ -0,0 +1,66 @@
+[
+ {"id": "disease", "parent": "#", "text": "Disease Phenotype", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "disease.d", "parent":"disease", "text": "Donor (normal)"},
+ {"id": "disease.b", "parent":"disease", "text": "BPH"},
+ {"id": "disease.c", "parent":"disease", "text": "Prostate Cancer"},
+ {"id": "demographics", "parent": "#", "text": "Demographics", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "ethnicity", "parent":"demographics", "text": "Ethnicity", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "ethn.aa", "parent":"ethnicity", "text": "African American"},
+ {"id": "ethn.as", "parent":"ethnicity", "text": "Asian"},
+ {"id": "ethn.ca", "parent":"ethnicity", "text": "Caucasian"},
+ {"id": "ethn.hi", "parent":"ethnicity", "text": "Hispanic"},
+ {"id": "ethn.uk", "parent":"ethnicity", "text": "Unknown Ethnicity"},
+ {"id": "age", "parent":"demographics", "text": "Age", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "age.40", "parent":"age", "text": "<40yo"},
+ {"id": "age.50", "parent":"age", "text": "41-50yo"},
+ {"id": "age.60", "parent":"age", "text": "51-60yo"},
+ {"id": "age.70", "parent":"age", "text": "61-70yo"},
+ {"id": "age.80", "parent":"age", "text": "71-80yo"},
+ {"id": "age.90", "parent":"age", "text": "81-90yo"},
+ {"id": "age.100", "parent":"age", "text": "91+yo"},
+ {"id": "age.uk", "parent":"age", "text": "Unknown Age"},
+ {"id": "clinical", "parent":"#", "text": "Clinical Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bmi", "parent":"clinical", "text": "BMI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bmi.uw", "parent":"bmi", "text": "Underweight"},
+ {"id": "bmi.nw", "parent":"bmi", "text": "Normal"},
+ {"id": "bmi.ow", "parent":"bmi", "text": "Overweight"},
+ {"id": "bmi.ob", "parent":"bmi", "text": "Obese"},
+ {"id": "bmi.vo", "parent":"bmi", "text": "Very Obese"},
+ {"id": "bmi.so", "parent":"bmi", "text": "Severely Obese"},
+ {"id": "bmi.uk", "parent":"bmi", "text": "Unknown BMI"},
+ {"id": "t2d", "parent":"clinical", "text": "Type 2 Diabetes", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "t2d.y", "parent":"t2d", "text": "Yes"},
+ {"id": "t2d.n", "parent":"t2d", "text": "No"},
+ {"id": "t2d.uk", "parent":"t2d", "text": "Unknown"},
+ {"id": "bph", "parent":"clinical", "text": "BPH Features", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bphsurgery", "parent":"bph", "text": "BPH Surgery", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "bphsurg.simp", "parent":"bphsurgery", "text": "Simple Prostatectomy"},
+ {"id": "bphsurg.turp", "parent":"bphsurgery", "text": "TURP"},
+ {"id": "bphsurg.uk", "parent":"bphsurgery", "text": "Unknown Surgery"},
+ {"id": "5ari", "parent":"bph", "text": "5ARI", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "5ari.y", "parent":"5ari", "text": "Yes 5ARI"},
+ {"id": "5ari.n", "parent":"5ari", "text": "No 5ARI"},
+ {"id": "5ari.uk", "parent":"5ari", "text": "Unknown 5ARI"},
+ {"id": "5aril", "parent":"bph", "text": "5ARI Length (months)", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "5aril.10", "parent":"5aril", "text": "<10mnths 5ARI"},
+ {"id": "5aril.20", "parent":"5aril", "text": "10-20mnths 5ARI"},
+ {"id": "5aril.30", "parent":"5aril", "text": "20+mnths 5ARI"},
+ {"id": "5aril.uk", "parent":"5aril", "text": "Unknown 5ARI"},
+ {"id": "5aril.na", "parent":"5aril", "text": "NA 5ARI"},
+ {"id": "prostatevol", "parent":"clinical", "text": "Prostate Volume", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "prvol.low", "parent":"prostatevol", "text": "Low Volumne"},
+ {"id": "prvol.med", "parent":"prostatevol", "text": "Medium Volume"},
+ {"id": "prvol.hi", "parent":"prostatevol", "text": "High Volume"},
+ {"id": "prvol.vhi", "parent":"prostatevol", "text": "Very High Volume"},
+ {"id": "prvol.uk", "parent":"prostatevol", "text": "Unknown Volume"},
+ {"id": "repo", "parent":"#", "text": "Repository", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "repo.pr", "parent":"repo", "text": "Prostate", "a_attr": { "class": "no_checkbox" }, "disabled": true},
+ {"id": "repo.pr.cry", "parent":"repo.pr", "text": "Pr Cryopreserved Cells"},
+ {"id": "repo.pr.ff", "parent":"repo.pr", "text": "Pr Flash Frozen Tissue"},
+ {"id": "repo.pr.ffpe", "parent":"repo.pr", "text": "Pr FFPE"},
+ {"id": "repo.pr.oct", "parent":"repo.pr", "text": "Pr OCT"},
+ {"id": "repo.bl", "parent":"repo", "text": "Bladder"},
+ {"id": "repo.sv", "parent":"repo", "text": "Seminal Vesicle"},
+ {"id": "repo.vd", "parent":"repo", "text": "Vas Deferencec"},
+ {"id": "repo.ut", "parent":"repo", "text": "Ureter"}
+]
\ No newline at end of file
diff --git a/data/repository/repository.json b/data/repository/repository.json
new file mode 100644
index 0000000000000000000000000000000000000000..d030e11d90493e54630eb7f60313c959f2a741d9
--- /dev/null
+++ b/data/repository/repository.json
@@ -0,0 +1,10152 @@
+[
+ {
+ "PatientID": "dws000001",
+ "Study ID": 1,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 62,
+ "Ethnicity": "Cauc",
+ "AUASS": 21,
+ "Peak flowrate": 6.1,
+ "Post void residual": 157,
+ "Prostate volume": 100,
+ "PSA": 9.62,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": 60,
+ "BMI": 29.1,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 286,
+ "HBA1c": 7.2,
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000002",
+ "Study ID": 2,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 65,
+ "Ethnicity": "Hisp",
+ "AUASS": "unknown",
+ "Peak flowrate": 4.1,
+ "Post void residual": 76,
+ "Prostate volume": 200,
+ "PSA": 10.9,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": 48,
+ "BMI": 29.9,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 164,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000003",
+ "Study ID": 3,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 70,
+ "Ethnicity": "Cauc",
+ "AUASS": 8,
+ "Peak flowrate": 4.1,
+ "Post void residual": 170,
+ "Prostate volume": 208.9,
+ "PSA": 2,
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 32.7,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000004",
+ "Study ID": 4,
+ "Disease Status": "BPH",
+ "BPH surgery": "TURP",
+ "Age": 61,
+ "Ethnicity": "Cauc",
+ "AUASS": 13,
+ "Peak flowrate": 7.7,
+ "Post void residual": 200,
+ "Prostate volume": 33,
+ "PSA": 1,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 28.2,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000005",
+ "Study ID": 5,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 83,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": "unknown",
+ "Post void residual": 457,
+ "Prostate volume": 138,
+ "PSA": 4.36,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 27.2,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 112,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 0,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000006",
+ "Study ID": 6,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 61,
+ "Ethnicity": "Cauc",
+ "AUASS": 17,
+ "Peak flowrate": 10.2,
+ "Post void residual": 620,
+ "Prostate volume": 117,
+ "PSA": 3.6,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 31.5,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 144,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000007",
+ "Study ID": 7,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 54,
+ "Ethnicity": "Hisp",
+ "AUASS": 17,
+ "Peak flowrate": "unknown",
+ "Post void residual": "unknown",
+ "Prostate volume": 111.7,
+ "PSA": 14.2,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 28.3,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 224,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 0,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000008",
+ "Study ID": 8,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 80,
+ "Ethnicity": "Cauc",
+ "AUASS": 17,
+ "Peak flowrate": 3.1,
+ "Post void residual": 146,
+ "Prostate volume": 140,
+ "PSA": 6.7,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": "unknown",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 27.8,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000009",
+ "Study ID": 9,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 73,
+ "Ethnicity": "Cauc",
+ "AUASS": 17,
+ "Peak flowrate": 10.3,
+ "Post void residual": 141,
+ "Prostate volume": 130,
+ "PSA": 8.92,
+ "Urinary retention": 1,
+ "5ARI": 1,
+ "5ARI length (months)": 17,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 31.8,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 169,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 0,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000010",
+ "Study ID": 10,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 67,
+ "Ethnicity": "Cauc",
+ "AUASS": 26,
+ "Peak flowrate": 2.6,
+ "Post void residual": 323,
+ "Prostate volume": 160,
+ "PSA": 9.2,
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 29.8,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 112,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000011",
+ "Study ID": 11,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 56,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": 3.3,
+ "Post void residual": 313,
+ "Prostate volume": 110,
+ "PSA": "unknown",
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 25.5,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 127,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000012",
+ "Study ID": 12,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 68,
+ "Ethnicity": "Cauc",
+ "AUASS": 31,
+ "Peak flowrate": 11.4,
+ "Post void residual": 545,
+ "Prostate volume": 150,
+ "PSA": 7.1,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 31.4,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 217,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000013",
+ "Study ID": 13,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 71,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": "unknown",
+ "Post void residual": "unknown",
+ "Prostate volume": 140,
+ "PSA": 3.2,
+ "Urinary retention": 1,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 30.3,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 121,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000014",
+ "Study ID": 14,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 60,
+ "Ethnicity": "AA",
+ "AUASS": 9,
+ "Peak flowrate": "unknown",
+ "Post void residual": "unknown",
+ "Prostate volume": 106.4,
+ "PSA": 5.74,
+ "Urinary retention": 0,
+ "5ARI": 0,
+ "5ARI length (months)": "na",
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 39.1,
+ "Type 2 diabetes": 0,
+ "Blood glucose": 95,
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000015",
+ "Study ID": 20,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 58,
+ "Ethnicity": "Cauc",
+ "AUASS": "unknown",
+ "Peak flowrate": 12.3,
+ "Post void residual": 219,
+ "Prostate volume": 158,
+ "PSA": 21.33,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": 60,
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 28.4,
+ "Type 2 diabetes": 1,
+ "Blood glucose": 133,
+ "HBA1c": 6.6,
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000016",
+ "Study ID": 24,
+ "Disease Status": "BPH",
+ "BPH surgery": "Simple",
+ "Age": 67,
+ "Ethnicity": "Cauc",
+ "AUASS": 19,
+ "Peak flowrate": 3.8,
+ "Post void residual": 147,
+ "Prostate volume": 126,
+ "PSA": 4.85,
+ "Urinary retention": 0,
+ "5ARI": 1,
+ "5ARI length (months)": 24,
+ "Alpha blocker": 1,
+ "Alpha blocker length (months)": "unknown",
+ "BMI": 26.2,
+ "Type 2 diabetes": 0,
+ "Blood glucose": "unknown",
+ "HBA1c": "unknown",
+ "Hyperlipidemia": 1,
+ "Hypertension": 1,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 1,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 0,
+ "Matching Seminal vesicle": 0,
+ "Matching vas deferens": 0,
+ "Matching ureter": 0
+ },
+ {
+ "PatientID": "dws000017",
+ "Study ID": 54,
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diff --git a/data/scRNAseq_huPr_D/updated_cleaned_json.json b/data/scRNAseq_huPr_D/updated_cleaned_json.json
new file mode 100644
index 0000000000000000000000000000000000000000..f3b30f44bde8fcc7cef7cf09052f6701d8043d32
--- /dev/null
+++ b/data/scRNAseq_huPr_D/updated_cleaned_json.json
@@ -0,0 +1,10154 @@
+[
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+ },
+ {
+ "PatientID": "bph00279",
+ "Study ID": "D31",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 27,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 20,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00280",
+ "Study ID": "D32",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 23,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 18,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00281",
+ "Study ID": "D33",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": null,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": null,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00282",
+ "Study ID": "D34",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": null,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 19,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00283",
+ "Study ID": "D35",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 29,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 20,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00284",
+ "Study ID": "D36",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": null,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 21,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00285",
+ "Study ID": "D37",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 29,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 24,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 1,
+ "Urine": 1,
+ "Buffy coat": 1,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00286",
+ "Study ID": "D38",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 25,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 21,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 1,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00287",
+ "Study ID": "D39",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 32,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 20,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00288",
+ "Study ID": "D40",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 40,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": null,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00289",
+ "Study ID": "D41",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 50,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 34,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 1,
+ "Urine": 1,
+ "Buffy coat": 1,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ },
+ {
+ "PatientID": "bph00290",
+ "Study ID": "D42",
+ "Disease Status": "Donor",
+ "BPH surgery": null,
+ "Age": 40,
+ "Ethnicity": null,
+ "AUASS": null,
+ "Peak flowrate": null,
+ "Post void residual": null,
+ "Prostate volume": 27,
+ "PSA": null,
+ "Urinary retention": null,
+ "5ARI": null,
+ "5ARI length (months)": null,
+ "Alpha blocker": 0,
+ "Alpha blocker length (months)": null,
+ "BMI": null,
+ "Type 2 diabetes": 0,
+ "Blood glucose": null,
+ "HBA1c": null,
+ "Hyperlipidemia": 0,
+ "Hypertension": 0,
+ "Serum": 0,
+ "Urine": 0,
+ "Buffy coat": 0,
+ "Cryopreserved single cells": 0,
+ "Flash frozen": 1,
+ "Paraffin block": 1,
+ "OCT block": 1,
+ "Matching bladder": 1,
+ "Matching Seminal vesicle": 1,
+ "Matching vas deferens": 1,
+ "Matching ureter": 1
+ }
+]
diff --git a/layouts/custom/contact.html b/layouts/custom/contact.html
index f04f7d132a1b364a50b7faad91063f4523bf8dfc..36f50cb56886613cb30d254561964a56bb07ed52 100644
--- a/layouts/custom/contact.html
+++ b/layouts/custom/contact.html
@@ -7,16 +7,14 @@
<div class="content">
<p style="text-align: center">
- Questions about our research or need a tip on one of our protocols?
- Interested in collaborations? Email us, mention any person, project, or
- activity of interest,and we will get back to you soon!
+ Questions about our research or need a tip on one of our protocols? Interested in collaborations? Email us,
+ mention any person, project, or activity of interest,and we will get back to you soon!
</p>
<hr>
<div style="text-align: center">
<iframe
src="https://www.google.com/maps/embed?pb=!1m18!1m12!1m3!1d3353.0540362781526!2d-96.84412528424524!3d32.81733318923467!2m3!1f0!2f0!3f0!3m2!1i1024!2i768!4f13.1!3m3!1m2!1s0x864e9c04b088e599%3A0x2e63ea34f8b2150b!2sUT%20Southwestern%20Medical%20Center!5e0!3m2!1sen!2sus!4v1576207208811!5m2!1sen!2sus"
- width="600" height="450" frameborder="0" style="border:0"
- allowfullscreen=""></iframe>
+ width="600" height="450" frameborder="0" style="border:0" allowfullscreen=""></iframe>
</div>
<hr>
<div style="text-align: center">
diff --git a/layouts/custom/hu.donor.deep.html b/layouts/custom/hu.donor.deep.html
index 6c253b5adb5d0c8346e1ba2dd4212fc8cba80250..c3c91ebe4344142f6acc2912ab14b5937b850c74 100644
--- a/layouts/custom/hu.donor.deep.html
+++ b/layouts/custom/hu.donor.deep.html
@@ -160,19 +160,19 @@
$(function () {
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
var selectedGene = $("#gene").autocomplete({
- source: genes.genes,
- maxResults: 10,
- maxShowItems: 10,
- minLength: 1,
+ source: genes.genes,
+ maxResults: 10,
+ maxShowItems: 10,
+ minLength: 1,
});
- });
- $("#analysis").click(function (event) {
+ });
+ $("#analysis").click(function (event) {
event.preventDefault();
var genes = {{ index .Site.Data.sc_data.hu_donor_pr_deep.genes }};
_gene = $("#gene").val().toUpperCase();
if ($.inArray(_gene, genes.genes) < 0) {
- alert("Gene " + _gene + " not exist in the data.")
- return
+ alert("Gene " + _gene + " not exist in the data.")
+ return
}
document.getElementById("label.gene").innerHTML = _gene
document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
@@ -186,6 +186,6 @@
var img = document.getElementById("img.ViolinBox");
img.src = "https://s3.us-east-2.amazonaws.com/images.gse117403.deep/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
return (_gene)
- });
+ });
</script>
</head>
\ No newline at end of file
diff --git a/layouts/custom/hu.donor.shallow.html b/layouts/custom/hu.donor.shallow.html
index 1fdd76bf935ea3cabf839c7110275e873f992d63..0e9cf0a32b357d2a839525b3353f06b9f7ce3740 100644
--- a/layouts/custom/hu.donor.shallow.html
+++ b/layouts/custom/hu.donor.shallow.html
@@ -1,191 +1,191 @@
{{ partial "header.html" . }}
<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
</div>
<div class="content">
- {{ .Content }}
+ {{ .Content }}
</div>
<style>
- .content {
- margin: 0;
- max-width: none;
- }
-
- .select {
- float: top;
- z-index: 1;
- top: 0px;
- background: #191818;
- overflow-x: hidden;
- padding: 8px 10px;
- }
-
- .columnS {
- float: left;
- text-align: center;
- width: 50%;
- }
-
- .columnF {
- float: left;
- text-align: center;
- width: 33.33%;
- }
-
- .row:after {
- content: "";
- display: table;
- clear: both;
- }
+ .content {
+ margin: 0;
+ max-width: none;
+ }
- img {
- max-width: 100%;
- height: auto;
- }
+ .select {
+ float: top;
+ z-index: 1;
+ top: 0px;
+ background: #191818;
+ overflow-x: hidden;
+ padding: 8px 10px;
+ }
- @media (max-width: 1000px) {
.columnS {
- text-align: right;
- width: 100%;
+ float: left;
+ text-align: center;
+ width: 50%;
}
.columnF {
- width: 100%;
+ float: left;
+ text-align: center;
+ width: 33.33%;
+ }
+
+ .row:after {
+ content: "";
+ display: table;
+ clear: both;
}
- br {
- display: none;
+ img {
+ max-width: 100%;
+ height: auto;
+ }
+
+ @media (max-width: 1000px) {
+ .columnS {
+ text-align: right;
+ width: 100%;
+ }
+
+ .columnF {
+ width: 100%;
+ }
+
+ br {
+ display: none;
+ }
}
- }
</style>
<body>
- <div class="select">
- <div class="columnS ui-widget">
- <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
- <br>
- <input id="gene" size="19">
- </div>
- <div class="columnS">
- <label for="populations" style="font-size:18px;">
- <b>Select a group of cell populations:</b>
- </label>
- <br>
- <select name="populations" id="populations">
- <option selected="selected" value="Population"> Cell Populations</option>
- <option>Lineage</option>
- <option value="Zone">Prostatic Zone</option>
- <option>Patient</option>
- </select>
- </div>
- <br>
- <div style="text-align:center">
- <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
- </div>
- <hr>
- <div>
- <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
- <br>
- <span style="font-size:16px;">
- Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from the
- prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were clustered and
- identified by correlation of their transcriptomes to known cell types. Gene expression can be compared by
- population identity, cell lineage, patient, or dissected prostatic zone. This is the original sequencing depth
- published.
- </span>
- </div>
- </div>
- <div align="center">
- <h1 id="label.gene">NO GENE SELECTED</h1>
- <h2 id="label.populations"></h2>
- <div class="columnF">
- <h4 id="label.ClusterVis">
- </h3>
- <div class="img">
- <img id="img.ClusterVis" src="" />
+ <div class="select">
+ <div class="columnS ui-widget">
+ <label for="gene" style="font-family:sans-serif; font-size:18px;"><b>Gene:</b></label>
+ <br>
+ <input id="gene" size="19">
</div>
- <br>
- </div>
- <div class="columnF">
- <h4 id="label.Feature">
- </h3>
- <div class="img">
- <img id="img.Feature" src="" />
+ <div class="columnS">
+ <label for="populations" style="font-size:18px;">
+ <b>Select a group of cell populations:</b>
+ </label>
+ <br>
+ <select name="populations" id="populations">
+ <option selected="selected" value="Population"> Cell Populations</option>
+ <option>Lineage</option>
+ <option value="Zone">Prostatic Zone</option>
+ <option>Patient</option>
+ </select>
</div>
<br>
+ <div style="text-align:center">
+ <button type="submit" id="analysis" class="btn btn-primary">Run Analysis</button>
+ </div>
+ <hr>
+ <div>
+ <span style="font-size:16px; font-weight:bold;">Experimental details:</span>
+ <br>
+ <span style="font-size:16px;">
+ Single Cell RNA-Sequencing was conducted on 32,194 cells from peripheral zone and transition zone from
+ the prostate of three 18-38 year old organ donors using the 10x Genomics platform. The cells were
+ clustered and identified by correlation of their transcriptomes to known cell types. Gene expression can
+ be compared by population identity, cell lineage, patient, or dissected prostatic zone. This is the
+ original sequencing depth published.
+ </span>
+ </div>
</div>
- <div class="columnF">
- <h4 id="label.ViolinBox">
- </h3>
- <div class="img">
- <img id="img.ViolinBox" src="" />
+ <div align="center">
+ <h1 id="label.gene">NO GENE SELECTED</h1>
+ <h2 id="label.populations"></h2>
+ <div class="columnF">
+ <h4 id="label.ClusterVis">
+ </h3>
+ <div class="img">
+ <img id="img.ClusterVis" src="" />
+ </div>
+ <br>
+ </div>
+ <div class="columnF">
+ <h4 id="label.Feature">
+ </h3>
+ <div class="img">
+ <img id="img.Feature" src="" />
+ </div>
+ <br>
+ </div>
+ <div class="columnF">
+ <h4 id="label.ViolinBox">
+ </h3>
+ <div class="img">
+ <img id="img.ViolinBox" src="" />
+ </div>
+ <br>
</div>
- <br>
</div>
- </div>
- <hr>
- <div align="left">
- <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
- <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
- target="_blank">Cell Reports</a></span></div>
- <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
- <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
- target="_blank">GEO:
- GSE117403</a></span></div>
- <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
- W-R8CM</a></span></div>
- </div>
+ <hr>
+ <div align="left">
+ <div><span style="font-size:18px; font-weight:bold;">Publication found at:</span></div>
+ <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=30566875"
+ target="_blank">Cell Reports</a></span></div>
+ <div><span style="font-size:18px; font-weight:bold;">Raw data found at:</span></div>
+ <div><span style="font-size:16px;"> <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403"
+ target="_blank">GEO:
+ GSE117403</a></span></div>
+ <div><span style="font-size:16px;"><a href="https://doi.org/10.25548/W-R8CM" target="_blank">GUDMAP:
+ W-R8CM</a></span></div>
+ </div>
</body>
{{ partial "footer.html" . }}
<head>
- <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
- <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
- <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
- <style>
- .ui-autocomplete {
- max-height: 200px;
- overflow-y: auto;
- overflow-x: hidden;
- }
- </style>
- <script>
- $(function () {
- $("#populations").selectmenu({ width: 230 });
- });
- $(function () {
- var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
- var selectedGene = $("#gene").autocomplete({
- source: genes.genes,
- maxResults: 10,
- maxShowItems: 10,
- minLength: 1,
- });
- });
- $("#analysis").click(function (event) {
- event.preventDefault();
- var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
- _gene = $("#gene").val().toUpperCase();
- if ($.inArray(_gene, genes.genes) < 0) {
- alert("Gene " + _gene + " not exist in the data.")
- return
- }
- document.getElementById("label.gene").innerHTML = _gene
- document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
- document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
- var img = document.getElementById("img.ClusterVis");
- img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
- document.getElementById("label.Feature").innerHTML = "Feature Plot"
- var img = document.getElementById("img.Feature");
- img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
- document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
- var img = document.getElementById("img.ViolinBox");
- img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
- return (_gene)
- });
- </script>
+ <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+ <style>
+ .ui-autocomplete {
+ max-height: 200px;
+ overflow-y: auto;
+ overflow-x: hidden;
+ }
+ </style>
+ <script>
+ $(function () {
+ $("#populations").selectmenu({ width: 230 });
+ });
+ $(function () {
+ var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
+ var selectedGene = $("#gene").autocomplete({
+ source: genes.genes,
+ maxResults: 10,
+ maxShowItems: 10,
+ minLength: 1,
+ });
+ });
+ $("#analysis").click(function (event) {
+ event.preventDefault();
+ var genes = {{ index .Site.Data.sc_data.hu_donor_pr_shallow.genes }};
+ _gene = $("#gene").val().toUpperCase();
+ if ($.inArray(_gene, genes.genes) < 0) {
+ alert("Gene " + _gene + " not exist in the data.")
+ return
+ }
+ document.getElementById("label.gene").innerHTML = _gene
+ document.getElementById("label.populations").innerHTML = "Separated by " + $("#populations").val().toUpperCase()
+ document.getElementById("label.ClusterVis").innerHTML = "Cluster Visualization"
+ var img = document.getElementById("img.ClusterVis");
+ img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/" + $("#populations").val() + "/tsne.png"
+ document.getElementById("label.Feature").innerHTML = "Feature Plot"
+ var img = document.getElementById("img.Feature");
+ img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/tsne/" + "genes/" + _gene + "_1.png"
+ document.getElementById("label.ViolinBox").innerHTML = "Violin Box Plot"
+ var img = document.getElementById("img.ViolinBox");
+ img.src = "https://s3.us-east-2.amazonaws.com/data.images.gse117403/images/ViolinBox/" + $("#populations").val() + "/genes/" + _gene + "_1.png"
+ return (_gene)
+ });
+ </script>
</head>
\ No newline at end of file
diff --git a/layouts/custom/people.html b/layouts/custom/people.html
index 382df21f7ad2fc6f61ba2a6b84c62c1836f35b30..b867f93deee0dce10074da1b7de7e1c5abd17fa1 100644
--- a/layouts/custom/people.html
+++ b/layouts/custom/people.html
@@ -10,18 +10,22 @@
.column {
float: left;
}
+
.left {
width: 25%;
}
+
.right {
width: 75%;
}
+
.row:after {
content: "";
display: table;
clear: both;
}
}
+
img.pic {
width: 175px;
padding: 7px;
diff --git a/layouts/custom/publications.html b/layouts/custom/publications.html
index 3fd85c124180a20eb4b40222ffe7c89fe5e593be..90f9dfecb3524cb05820c06a6c031b4693f821e6 100644
--- a/layouts/custom/publications.html
+++ b/layouts/custom/publications.html
@@ -5,12 +5,15 @@
.column {
float: left;
}
+
.left {
width: 25%;
}
+
.right {
width: 75%;
}
+
.row:after {
content: "";
display: table;
@@ -26,35 +29,33 @@
<br>
<div>
{{ range first 10 (.Pages.ByParam "odate" ).Reverse }}
- <div class="row">
- <div class="column left">
- <img src="images/{{.Params.ppic}}" alt="" width="100px;"
- style="border:5px double black; border-radius:20%;">
- </div>
- <div class="column right">
- <h3>{{.Params.pname}}</h3>
- </div>
+ <div class="row">
+ <div class="column left">
+ <img src="images/{{.Params.ppic}}" alt="" width="100px;"
+ style="border:5px double black; border-radius:20%;">
+ </div>
+ <div class="column right">
+ <h3>{{.Params.pname}}</h3>
</div>
- {{ if not (eq .Params.ppubmed "") }}
- <h4><i><a
- href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}"
- target="_blank">
- {{else}}
- <h4><i><a href="{{.Params.plink}}">
- {{end}}
- {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
- {{ range first 1 .Params.prepo }}
- {{ if not (eq .title "") }}
+ </div>
+ {{ if not (eq .Params.ppubmed "") }}
+ <h4><i><a href="https://www.ncbi.nlm.nih.gov/pubmed?term={{.Params.ppubmed}}" target="_blank">
+ {{else}}
+ <h4><i><a href="{{.Params.plink}}">
+ {{end}}
+ {{.Params.pauthor}}, {{.Params.pjournal}},{{.Params.pdate}}</a></i></h4>
+ {{ range first 1 .Params.prepo }}
+ {{ if not (eq .title "") }}
<u>Data Repository:</u><br>
- {{end}}
- {{end}}
- {{ range .Params.prepo }}
- {{ if not (eq .title "") }}
+ {{end}}
+ {{end}}
+ {{ range .Params.prepo }}
+ {{ if not (eq .title "") }}
<a href="{{.loc}}" target="_blank">{{.title}}</a><br>
- {{end}}
- {{end}}
- <hr><br>
- {{end}}
+ {{end}}
+ {{end}}
+ <hr><br>
+ {{end}}
</div>
</div>
diff --git a/layouts/custom/repository.html b/layouts/custom/repository.html
new file mode 100644
index 0000000000000000000000000000000000000000..5af08b58b009361309c3efa3640932dac67bf585
--- /dev/null
+++ b/layouts/custom/repository.html
@@ -0,0 +1,900 @@
+{{ partial "header.html" . }}
+
+<div class="header">
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
+</div>
+<div class="content">
+ {{ .Content }}
+</div>
+
+<style>
+ .pure-menu-heading {
+ font-family: sans-serif;
+ line-height: 1.15;
+ }
+
+ .pure-menu {
+ font-family: sans-serif;
+ line-height: 1.15;
+ }
+
+ .pure-menu-social {
+ font-family: sans-serif;
+ line-height: 1.15;
+ }
+
+ .small-print {
+ color: #777;
+ font-family: sans-serif;
+ }
+
+ .content {
+ margin: 0;
+ max-width: none;
+ }
+
+ .select {
+ float: top;
+ z-index: 1;
+ top: 0px;
+ color: #777;
+ background: #191818;
+ overflow-x: hidden;
+ padding: 8px 10px;
+ }
+
+ .panel_canvas {
+ width: 175px;
+ }
+
+ .icon {
+ font-size: 50px;
+ padding: 5px;
+ }
+
+ th,
+ td {
+ padding: 5px 15px;
+ text-align: center;
+ }
+
+ .no_checkbox>i.jstree-checkbox {
+ display: none
+ }
+</style>
+
+<head>
+ <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css">
+ <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js"></script>
+ <link rel="stylesheet" href="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/themes/smoothness/jquery-ui.css">
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jqueryui/1.12.1/jquery-ui.min.js"></script>
+ <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/themes/default/style.min.css">
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/jstree/3.2.1/jstree.min.js"></script>
+ <script src="https://cdnjs.cloudflare.com/ajax/libs/Chart.js/2.5.0/Chart.min.js"></script>
+ <script>
+ $(function () {
+ var repo = {{ index .Site.Data.repository.repository }}
+ var filters = {{ index .Site.Data.repository.filters }}
+ $("#jstree").jstree({
+ "core": {
+ "data": filters,
+ "themes": {
+ "theme": "default",
+ "dots": false,
+ "icons": false
+ },
+ },
+ "checkbox": {
+ "keep_selected_style": false,
+ cascade: "",
+ three_state: false,
+ whole_node: false,
+ tie_selection: false
+ },
+ "plugins": ["themes", "checkbox"]
+ })
+
+ $("#jstree").bind("check_node.jstree uncheck_node.jstree", function (e, data) {
+ var checked = $("#jstree").jstree("get_checked")
+ var filter = []
+ for (i = 0; i < checked.length; i++) {
+ for (j = 0; j < filters.length; j++) {
+ if (checked[i] == filters[j].id) {
+ filter.push(filters[j].text)
+ }
+ }
+ }
+ filtered = filterRepo(repo, checked)
+ filterRepoGroups_out = filterRepoGroups(repo, filtered)
+ filtered_dis = filterRepoGroups_out[0]
+ filtered_bmi = filterRepoGroups_out[1]
+ filtered_t2d = filterRepoGroups_out[2]
+ filtered_eth = filterRepoGroups_out[3]
+ filtered_age = filterRepoGroups_out[4]
+ filtered_prv = filterRepoGroups_out[5]
+ filtered_psa = filterRepoGroups_out[6]
+ document.getElementById("total").innerHTML = filtered.length
+ if (checked.length == 0) {
+ document.getElementById("filters").innerHTML = "NO"
+ } else {
+ document.getElementById("filters").innerHTML = filter
+ }
+ filterDoughnut_out = filterDoughnut(filtered_bmi, filtered_t2d, filtered_eth, filtered_age, filtered_prv, filtered_psa)
+ doughnut_data_dis = filterDoughnut_out[0]
+ doughnut_data_bmi = filterDoughnut_out[1]
+ doughnut_data_t2d = filterDoughnut_out[2]
+ doughnut_data_eth = filterDoughnut_out[3]
+ doughnut_data_age = filterDoughnut_out[4]
+ doughnut_data_prv = filterDoughnut_out[5]
+ doughnut_data_psa = filterDoughnut_out[6]
+ dis.destroy()
+ dis = new Chart(document.getElementById("doughnut-dis"), { type: "doughnut", data: doughnut_data_dis, options: doughnut_options })
+ bmi.destroy()
+ bmi = new Chart(document.getElementById("doughnut-bmi"), { type: "doughnut", data: doughnut_data_bmi, options: doughnut_options })
+ t2d.destroy()
+ t2d = new Chart(document.getElementById("doughnut-t2d"), { type: "doughnut", data: doughnut_data_t2d, options: doughnut_options })
+ eth.destroy()
+ eth = new Chart(document.getElementById("doughnut-eth"), { type: "doughnut", data: doughnut_data_eth, options: doughnut_options })
+ age.destroy()
+ age = new Chart(document.getElementById("doughnut-age"), { type: "doughnut", data: doughnut_data_age, options: doughnut_options })
+ prv.destroy()
+ prv = new Chart(document.getElementById("doughnut-prv"), { type: "doughnut", data: doughnut_data_prv, options: doughnut_options })
+ psa.destroy()
+ psa = new Chart(document.getElementById("doughnut-psa"), { type: "doughnut", data: doughnut_data_psa, options: doughnut_options })
+ tableData(repo, filtered)
+ })
+ checked = []
+ filtered = filterRepo(repo, checked)
+ filterRepoGroups_out = filterRepoGroups(repo, filtered)
+ filtered_dis = filterRepoGroups_out[0]
+ filtered_bmi = filterRepoGroups_out[1]
+ filtered_t2d = filterRepoGroups_out[2]
+ filtered_eth = filterRepoGroups_out[3]
+ filtered_age = filterRepoGroups_out[4]
+ filtered_prv = filterRepoGroups_out[5]
+ filtered_psa = filterRepoGroups_out[6]
+ document.getElementById("total").innerHTML = filtered.length
+ document.getElementById("filters").innerHTML = "NO"
+ filterDoughnut_out = filterDoughnut(filtered_bmi, filtered_t2d, filtered_eth, filtered_age, filtered_prv, filtered_psa)
+ doughnut_data_dis = filterDoughnut_out[0]
+ doughnut_data_bmi = filterDoughnut_out[1]
+ doughnut_data_t2d = filterDoughnut_out[2]
+ doughnut_data_eth = filterDoughnut_out[3]
+ doughnut_data_age = filterDoughnut_out[4]
+ doughnut_data_prv = filterDoughnut_out[5]
+ doughnut_data_psa = filterDoughnut_out[6]
+ dis = new Chart(document.getElementById("doughnut-dis"), { type: "doughnut", data: doughnut_data_dis, options: doughnut_options })
+ bmi = new Chart(document.getElementById("doughnut-bmi"), { type: "doughnut", data: doughnut_data_bmi, options: doughnut_options })
+ t2d = new Chart(document.getElementById("doughnut-t2d"), { type: "doughnut", data: doughnut_data_t2d, options: doughnut_options })
+ eth = new Chart(document.getElementById("doughnut-eth"), { type: "doughnut", data: doughnut_data_eth, options: doughnut_options })
+ age = new Chart(document.getElementById("doughnut-age"), { type: "doughnut", data: doughnut_data_age, options: doughnut_options })
+ prv = new Chart(document.getElementById("doughnut-prv"), { type: "doughnut", data: doughnut_data_prv, options: doughnut_options })
+ psa = new Chart(document.getElementById("doughnut-psa"), { type: "doughnut", data: doughnut_data_psa, options: doughnut_options })
+
+ tableData(repo, filtered)
+ })
+ var doughnut_options = {
+ responsive: true,
+ legend: {
+ display: false
+ }
+ }
+ function filterRepo(repo, checked) {
+ filtered = []
+ filtered_dis = []
+ filtered_eth = []
+ filtered_age = []
+ filtered_bmi = []
+ filtered_t2d = []
+ filtered_bphsurg = []
+ filtered_ari = []
+ filtered_aril = []
+ filtered_prvol = []
+ filtered_repo_pr_cry = []
+ filtered_repo_pr_ff = []
+ filtered_repo_pr_ffpe = []
+ filtered_repo_pr_oct = []
+ filtered_repo_bl = []
+ filtered_repo_sv = []
+ filtered_repo_vd = []
+ filtered_repo_ut = []
+ for (i = 0; i < repo.length; i++) {
+ filtered.push(repo[i].PatientID)
+ if (checked.includes("disease.d")) {
+ if (repo[i]["Disease Status"] == "Donor") {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("disease.b")) {
+ if (repo[i]["Disease Status"] == "BPH") {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("disease.c")) {
+ if (repo[i]["Disease Status"] == "Cancer") {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("disease.d") && !checked.includes("disease.b") && !checked.includes("disease.c")) {
+ filtered_dis.push(repo[i].PatientID)
+ }
+ if (checked.includes("ethn.aa")) {
+ if (repo[i].Ethnicity == "AA") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.as")) {
+ if (repo[i].Ethnicity == "Asian") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.ca")) {
+ if (repo[i].Ethnicity == "Cauc") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.hi")) {
+ if (repo[i].Ethnicity == "Hisp") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("ethn.uk")) {
+ if (repo[i].Ethnicity == "unknown") {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("ethn.aa") && !checked.includes("ethn.as") && !checked.includes("ethn.ca") && !checked.includes("ethn.hi") && !checked.includes("ethn.uk")) {
+ filtered_eth.push(repo[i].PatientID)
+ }
+ if (checked.includes("age.40")) {
+ if (repo[i].Age < 41) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.50")) {
+ if (repo[i].Age >= 41 && repo[i].Age < 51) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.60")) {
+ if (repo[i].Age >= 51 && repo[i].Age < 61) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.70")) {
+ if (repo[i].Age >= 61 && repo[i].Age < 71) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.80")) {
+ if (repo[i].Age >= 71 && repo[i].Age < 81) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.90")) {
+ if (repo[i].Age >= 81 && repo[i].Age < 91) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.100")) {
+ if (repo[i].Age >= 91) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("age.uk")) {
+ if (repo[i].Age == "unknown") {
+ filtered_age.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("age.40") && !checked.includes("age.50") && !checked.includes("age.60") && !checked.includes("age.70") && !checked.includes("age.80") && !checked.includes("age.90") && !checked.includes("age.100") && !checked.includes("age.uk")) {
+ filtered_age.push(repo[i].PatientID)
+ }
+ if (checked.includes("bmi.uw")) {
+ if (repo[i].BMI < 18.5) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.nw")) {
+ if (repo[i].BMI >= 18.5 && repo[i].BMI < 25) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.ow")) {
+ if (repo[i].BMI >= 25 && repo[i].BMI < 30) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.ob")) {
+ if (repo[i].BMI >= 30 && repo[i].BMI < 35) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.vo")) {
+ if (repo[i].BMI >= 35 && repo[i].BMI < 40) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.so")) {
+ if (repo[i].BMI >= 40) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bmi.uk")) {
+ if (repo[i].BMI == "unknown") {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("bmi.uw") && !checked.includes("bmi.nw") && !checked.includes("bmi.ow") && !checked.includes("bmi.ob") && !checked.includes("bmi.vo") && !checked.includes("bmi.so") && !checked.includes("bmi.uk")) {
+ filtered_bmi.push(repo[i].PatientID)
+ }
+ if (checked.includes("t2d.y")) {
+ if (repo[i]["Type 2 diabetes"] == 1) {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("t2d.n")) {
+ if (repo[i]["Type 2 diabetes"] == 0) {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("t2d.uk")) {
+ if (repo[i]["Type 2 diabetes"] == "unknown") {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("t2d.y") && !checked.includes("t2d.n") && !checked.includes("t2d.uk")) {
+ filtered_t2d.push(repo[i].PatientID)
+ }
+ if (checked.includes("bphsurg.simp")) {
+ if (repo[i]["BPH surgery"] == "Simple") {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bphsurg.turp")) {
+ if (repo[i]["BPH surgery"] == "TURP") {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("bphsurg.uk")) {
+ if (repo[i]["BPH surgery"] == "unknown") {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("bphsurg.simp") && !checked.includes("bphsurg.turp") && !checked.includes("bphsurg.uk")) {
+ filtered_bphsurg.push(repo[i].PatientID)
+ }
+ if (checked.includes("5ari.y")) {
+ if (repo[i]["5ARI"] == 1) {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5ari.n")) {
+ if (repo[i]["5ARI"] == 0) {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5ari.uk")) {
+ if (repo[i]["5ARI"] == "unknown") {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("5ari.y") && !checked.includes("5ari.n") && !checked.includes("5ari.uk")) {
+ filtered_ari.push(repo[i].PatientID)
+ }
+ if (checked.includes("5aril.10")) {
+ if (repo[i]["5ARI length (months)"] < 10) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.20")) {
+ if (repo[i]["5ARI length (months)"] >= 10 && repo[i]["5ARI length (months)"] < 20) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.30")) {
+ if (repo[i]["5ARI length (months)"] >= 20) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.uk")) {
+ if (repo[i]["5ARI length (months)"] == "unknown") {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("5aril.na")) {
+ if (repo[i]["5ARI length (months)"] == "na") {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("5aril.10") && !checked.includes("5aril.20") && !checked.includes("5aril.30") && !checked.includes("5aril.uk") && !checked.includes("5aril.na")) {
+ filtered_aril.push(repo[i].PatientID)
+ }
+ if (checked.includes("prvol.low")) {
+ if (repo[i]["Prostate volume"] < 31) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.med")) {
+ if (repo[i]["Prostate volume"] >= 31 && repo[i]["Prostate volume"] < 81) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.hi")) {
+ if (repo[i]["Prostate volume"] >= 81 && repo[i]["Prostate volume"] < 121) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.vhi")) {
+ if (repo[i]["Prostate volume"] >= 121) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (checked.includes("prvol.uk")) {
+ if (repo[i]["Prostate volume"] == "unknown") {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ }
+ if (!checked.includes("prvol.low") && !checked.includes("prvol.med") && !checked.includes("prvol.hi") && !checked.includes("prvol.vhi") && !checked.includes("prvol.uk")) {
+ filtered_prvol.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.cry")) {
+ if (repo[i]["Cryopreserved single cells"] == 1) {
+ filtered_repo_pr_cry.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_cry.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.ff")) {
+ if (repo[i]["Flash frozen"] == 1) {
+ filtered_repo_pr_ff.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_ff.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.ffpe")) {
+ if (repo[i]["Paraffin block"] == 1) {
+ filtered_repo_pr_ffpe.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_ffpe.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.pr.oct")) {
+ if (repo[i]["OCT block"] == 1) {
+ filtered_repo_pr_oct.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_pr_oct.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.bl")) {
+ if (repo[i]["Matching bladder"] == 1) {
+ filtered_repo_bl.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_bl.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.sv")) {
+ if (repo[i]["Matching Seminal vesicle"] == 1) {
+ filtered_repo_sv.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_sv.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.vd")) {
+ if (repo[i]["Matching vas deferens"] == 1) {
+ filtered_repo_vd.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_vd.push(repo[i].PatientID)
+ }
+ if (checked.includes("repo.ut")) {
+ if (repo[i]["Matching ureter"] == 1) {
+ filtered_repo_ut.push(repo[i].PatientID)
+ }
+ } else {
+ filtered_repo_ut.push(repo[i].PatientID)
+ }
+ }
+ filtered = intersect(filtered, filtered_dis)
+ filtered = intersect(filtered, filtered_eth)
+ filtered = intersect(filtered, filtered_age)
+ filtered = intersect(filtered, filtered_bmi)
+ filtered = intersect(filtered, filtered_t2d)
+ filtered = intersect(filtered, filtered_bphsurg)
+ filtered = intersect(filtered, filtered_ari)
+ filtered = intersect(filtered, filtered_aril)
+ filtered = intersect(filtered, filtered_prvol)
+ filtered = intersect(filtered, filtered_repo_pr_cry)
+ filtered = intersect(filtered, filtered_repo_pr_ff)
+ filtered = intersect(filtered, filtered_repo_pr_ffpe)
+ filtered = intersect(filtered, filtered_repo_pr_oct)
+ filtered = intersect(filtered, filtered_repo_bl)
+ filtered = intersect(filtered, filtered_repo_sv)
+ filtered = intersect(filtered, filtered_repo_vd)
+ filtered = intersect(filtered, filtered_repo_ut)
+
+ filtered = filtered.filter(onlyUnique)
+ if (checked.length == 0) {
+ filtered = []
+ for (i = 0; i < repo.length; i++) {
+ filtered.push(repo[i].PatientID)
+ }
+ }
+
+ document.getElementById("test").innerHTML = ""
+
+ return filtered
+ }
+ function filterRepoGroups(repo, filtered) {
+ filtered_dis = []
+ filtered_dis_d = []
+ filtered_dis_b = []
+ filtered_dis_c = []
+ filtered_bmi = []
+ filtered_bmi_uw = []
+ filtered_bmi_nw = []
+ filtered_bmi_ow = []
+ filtered_bmi_ob = []
+ filtered_bmi_vo = []
+ filtered_bmi_so = []
+ filtered_bmi_uk = []
+ filtered_t2d = []
+ filtered_t2d_no = []
+ filtered_t2d_ys = []
+ filtered_t2d_uk = []
+ filtered_eth = []
+ filtered_eth_aa = []
+ filtered_eth_as = []
+ filtered_eth_ca = []
+ filtered_eth_hi = []
+ filtered_eth_uk = []
+ filtered_eth = []
+ filtered_eth_aa = []
+ filtered_eth_as = []
+ filtered_eth_ca = []
+ filtered_eth_hi = []
+ filtered_eth_uk = []
+ filtered_age = []
+ filtered_age_40 = []
+ filtered_age_50 = []
+ filtered_age_60 = []
+ filtered_age_70 = []
+ filtered_age_80 = []
+ filtered_age_90 = []
+ filtered_age_100 = []
+ filtered_age_uk = []
+ filtered_prv = []
+ filtered_prv_40 = []
+ filtered_prv_50 = []
+ filtered_prv_60 = []
+ filtered_prv_uk = []
+ filtered_psa = []
+ filtered_psa_nm = []
+ filtered_psa_lr = []
+ filtered_psa_hr = []
+ filtered_psa_uk = []
+ for (i = 0; i < repo.length; i++) {
+ if (filtered.includes(repo[i].PatientID)) {
+ if (repo[i]["Disease Status"] == "Donor") {
+ filtered_dis_d.push(repo[i].PatientID)
+ }
+ if (repo[i]["Disease Status"] == "BPH") {
+ filtered_dis_b.push(repo[i].PatientID)
+ }
+ if (repo[i]["Disease Status"] == "Cancer") {
+ filtered_dis_c.push(repo[i].PatientID)
+ }
+
+ if (repo[i].BMI < 18.5) {
+ filtered_bmi_uw.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 18.5 && repo[i].BMI < 25) {
+ filtered_bmi_nw.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 25 && repo[i].BMI < 30) {
+ filtered_bmi_ow.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 30 && repo[i].BMI < 35) {
+ filtered_bmi_ob.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 35 && repo[i].BMI < 40) {
+ filtered_bmi_vo.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI >= 40) {
+ filtered_bmi_so.push(repo[i].PatientID)
+ }
+ if (repo[i].BMI == "unknown") {
+ filtered_bmi_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i]["Type 2 diabetes"] == 0) {
+ filtered_t2d_no.push(repo[i].PatientID)
+ }
+ if (repo[i]["Type 2 diabetes"] == 1) {
+ filtered_t2d_ys.push(repo[i].PatientID)
+ }
+ if (repo[i]["Type 2 diabetes"] == "unknown") {
+ filtered_t2d_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i].Ethnicity == "AA") {
+ filtered_eth_aa.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "Asian") {
+ filtered_eth_as.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "Cauc") {
+ filtered_eth_ca.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "Hisp") {
+ filtered_eth_hi.push(repo[i].PatientID)
+ }
+ if (repo[i].Ethnicity == "unknown") {
+ filtered_eth_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i].Age < 41) {
+ filtered_age_40.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 41 && repo[i].Age < 51) {
+ filtered_age_50.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 51 && repo[i].Age < 61) {
+ filtered_age_60.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 61 && repo[i].Age < 71) {
+ filtered_age_70.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 71 && repo[i].Age < 81) {
+ filtered_age_80.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 81 && repo[i].Age < 91) {
+ filtered_age_90.push(repo[i].PatientID)
+ }
+ if (repo[i].Age >= 91) {
+ filtered_age_100.push(repo[i].PatientID)
+ }
+ if (repo[i].Age == "unknown") {
+ filtered_age_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i]["Prostate volume"] < 41) {
+ filtered_prv_40.push(repo[i].PatientID)
+ }
+ if (repo[i]["Prostate volume"] >= 41 && repo[i]["Prostate volume"] < 51) {
+ filtered_prv_50.push(repo[i].PatientID)
+ }
+ if (repo[i]["Prostate volume"] >= 51) {
+ filtered_prv_60.push(repo[i].PatientID)
+ }
+ if (repo[i]["Prostate volume"] == "unknown") {
+ filtered_prv_uk.push(repo[i].PatientID)
+ }
+
+ if (repo[i].PSA < 1) {
+ filtered_psa_nm.push(repo[i].PatientID)
+ }
+ if (repo[i].PSA >= 1 && repo[i].PSA < 3) {
+ filtered_psa_lr.push(repo[i].PatientID)
+ }
+ if (repo[i].PSA >= 3) {
+ filtered_psa_hr.push(repo[i].PatientID)
+ }
+ if (repo[i].PSA == "unknown") {
+ filtered_psa_uk.push(repo[i].PatientID)
+ }
+ }
+ }
+ filtered_dis = [filtered_dis_d.length, filtered_dis_b.length, filtered_dis_c.length]
+ filtered_bmi = [filtered_bmi_uw.length, filtered_bmi_nw.length, filtered_bmi_ow.length, filtered_bmi_ob.length, filtered_bmi_vo.length, filtered_bmi_so.length, filtered_bmi_uk.length]
+ filtered_t2d = [filtered_t2d_no.length, filtered_t2d_ys.length, filtered_t2d_uk.length]
+ filtered_eth = [filtered_eth_aa.length, filtered_eth_as.length, filtered_eth_ca.length, filtered_eth_hi.length, filtered_eth_uk.length]
+ filtered_age = [filtered_age_40.length, filtered_age_50.length, filtered_age_60.length, filtered_age_70.length, filtered_age_80.length, filtered_age_90.length, filtered_age_100.length, filtered_age_uk.length]
+ filtered_prv = [filtered_prv_40.length, filtered_prv_50.length, filtered_prv_60.length, filtered_prv_uk.length]
+ filtered_psa = [filtered_psa_nm.length, filtered_psa_lr.length, filtered_psa_hr.length, filtered_psa_uk.length]
+
+ return [
+ filtered_dis,
+ filtered_bmi,
+ filtered_t2d,
+ filtered_eth,
+ filtered_age,
+ filtered_prv,
+ filtered_psa
+ ]
+ }
+ function filterDoughnut(filtered_bmi, filtered_t2d, filtered_eth, filtered_age, filtered_prv, filtered_psa) {
+ doughnut_data_dis = []
+ doughnut_data_bmi = []
+ doughnut_data_t2d = []
+ doughnut_data_eth = []
+ doughnut_data_age = []
+ doughnut_data_prv = []
+ doughnut_data_psa = []
+ doughnut_data_dis = {
+ labels: ["Donor (normal)", "BPH", "Prostate Cancer"],
+ datasets: [{
+ data: filtered_dis,
+ backgroundColor: ["#440154", "#21908C", "#FDE725"]
+ }]
+ }
+ doughnut_data_bmi = {
+ labels: ["Underweight", "Normal Weight", "Overweight", "Obese", "Very Obese", "Severely Obese", "Unknown"],
+ datasets: [{
+ data: filtered_bmi,
+ backgroundColor: ["#440154", "#443A83", "#31688E", "#21908C", "#35B779", "#8FD744", "#FDE725"]
+ }]
+ }
+ doughnut_data_t2d = {
+ labels: ["No", "Yes", "Unknown"],
+ datasets: [{
+ data: filtered_t2d,
+ backgroundColor: ["#440154", "#21908C", "#FDE725"]
+ }]
+ }
+ doughnut_data_eth = {
+ labels: ["African American", "Asian", "Caucasian", "Hispanic", "Unknown"],
+ datasets: [{
+ data: filtered_eth,
+ backgroundColor: ["#440154", "#3B528B", "#21908C", "#5DC863", "#FDE725"]
+ }]
+ }
+ doughnut_data_age = {
+ labels: ["0-40yo", "41-50yo", "51-60yo", "61-70yo", "71-80yo", "81-90yo", "91+yo", "Unknown"],
+ datasets: [{
+ data: filtered_age,
+ backgroundColor: ["#440154", "#46337E", "#365C8D", "#277F8E", "#1FA187", "#4AC16D", "#9FDA3A", "#FDE725"]
+ }]
+ }
+ doughnut_data_prv = {
+ labels: ["0-40cc", "41-50cc", "50+cc", "Unknown"],
+ datasets: [{
+ data: filtered_prv,
+ backgroundColor: ["#440154", "#31688E", "#35B779", "#FDE725"]
+ }]
+ }
+ doughnut_data_psa = {
+ labels: ["Normal", "Low Risk", "High Risk", "Unknown"],
+ datasets: [{
+ data: filtered_psa,
+ backgroundColor: ["#440154", "#31688E", "#35B779", "#FDE725"]
+ }]
+ }
+
+ return [
+ doughnut_data_dis,
+ doughnut_data_bmi,
+ doughnut_data_t2d,
+ doughnut_data_eth,
+ doughnut_data_age,
+ doughnut_data_prv,
+ doughnut_data_psa
+ ]
+ }
+ function tableData(repo, fitered) {
+ let table = document.getElementById("samplesTable")
+ while (table.rows.length > 1) {
+ table.deleteRow(-1);
+ }
+ for (i = 0; i < repo.length; i++) {
+ if (filtered.includes(repo[i].PatientID)) {
+ let newRow = table.insertRow(-1)
+ var row_ds = newRow.insertCell(0)
+ var row_si = newRow.insertCell(1)
+ var row_ag = newRow.insertCell(2)
+ var row_et = newRow.insertCell(3)
+ row_ds.innerHTML = repo[i]["Disease Status"]
+ row_si.innerHTML = repo[i]["Study ID"]
+ row_ag.innerHTML = repo[i].Age
+ row_et.innerHTML = repo[i].Ethnicity
+ }
+ }
+ }
+ function onlyUnique(value, index, self) {
+ return self.indexOf(value) === index
+ }
+ function intersect(a, b) {
+ var t;
+ if (b.length > a.length) t = b, b = a, a = t;
+ return a.filter(function (e) {
+ return b.indexOf(e) > -1;
+ });
+ }
+ </script>
+</head>
+
+<body>
+ <div class="select">
+ <div id="jstree"></div>
+ </div>
+ <br>
+ <div class="container" style="max-width: none;">
+ <div class="row">
+ <div class="col-8" style="color: grey; background-color: #191818;">
+ <h4 id="total"></h4>
+ <h5>Patients</h5>
+ </div>
+ <div class="col-4 text-right" style="color: grey; background-color: #191818;">
+ <i class='fa fa-user icon'></i>
+ </div>
+ </div>
+ <div class="row">
+ <div class="col-8" style="color: grey; background-color: #191818;">
+ <h4 id="filters"></h4>
+ <h5>Filters</h5>
+ </div>
+ <div class="col-4 text-right" style="color: grey; background-color: #191818;">
+ <i class='fa fa-filter icon'></i>
+ </div>
+ </div>
+ </div>
+ <p id="test">Test</p>
+ <hr>
+ <div class="container" align=center style="max-width: none;">
+ <div class="row">
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Disease Status</p>
+ <hr>
+ <canvas id="doughnut-dis" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>BMI</p>
+ <hr>
+ <canvas id="doughnut-bmi" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Type 2 Diabetes</p>
+ <hr>
+ <canvas id="doughnut-t2d" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Ethnicity</p>
+ <hr>
+ <canvas id="doughnut-eth" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Age</p>
+ <hr>
+ <canvas id="doughnut-age" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>Prostate Volume</p>
+ <hr>
+ <canvas id="doughnut-prv" width="150" height="150"></canvas>
+ </div>
+ </div>
+ <div class="col">
+ <div class="panel_canvas" style="text-align:center;">
+ <p>PSA</p>
+ <hr>
+ <canvas id="doughnut-psa" width="150" height="150"></canvas>
+ </div>
+ </div>
+ </div>
+ </div>
+ <hr>
+ <div class="container" align=center style="max-width: none;">
+ <table id="samplesTable" border="1">
+ <tr>
+ <th>Disease</th>
+ <th>ID</th>
+ <th>Age</th>
+ <th>Ethnicity</th>
+ </tr>
+ </table>
+ </div>
+</body>
+
+{{ partial "footer.html" . }}
\ No newline at end of file
diff --git a/layouts/custom/research.html b/layouts/custom/research.html
index e1c9ca34f87c47aea7697aa57ba12600fdf8d698..d2dc31dcef37a8e0fa7398a300c3abe7c95d3e8d 100644
--- a/layouts/custom/research.html
+++ b/layouts/custom/research.html
@@ -11,28 +11,33 @@
display: table;
clear: both;
}
+
div.fig {
padding: 1px;
border: 1px solid black;
margin: auto;
background-color: LightGrey;
}
+
div.fig img {
width: 500px;
max-width: 100%;
height: auto;
padding: 1px;
}
+
div.lab {
text-align: justify;
padding-left: 10px;
padding-right: 10px;
}
+
@media (min-width: 1000px) {
div.fig {
float: left;
margin: 1px 10px 1px 1px;
}
+
br {
display: none;
}
@@ -42,41 +47,30 @@
<div class="section">
<H1 align="center">Overview</H1>
<p style="text-align:justify; font-size:18px">
- The main goals of the Strand lab are to create accurate cellular
- atlases of the human and mouse lower
- urinary tract, characterize the molecular and cellular alterations
- in human lower urinary tract disease, and
+ The main goals of the Strand lab are to create accurate cellular atlases of the human and mouse lower
+ urinary tract, characterize the molecular and cellular alterations in human lower urinary tract disease, and
build appropriate models of the human disease in novel mouse models.
</p>
</div>
<div class="section">
<H1 align="center">Benign Prostatic Hyperplasia</H1>
<div class="fig" style="max-width:250px">
- <img src="/research.images/prostate.jpg" alt="prostate" class="img"
- />
+ <img src="/research.images/prostate.jpg" alt="prostate" class="img" />
<div class="lab">
- <p>Cross-section of a prostate gland, showing the transition
- zone (TZ) and the peripheral zone (PZ)</p>
+ <p>Cross-section of a prostate gland, showing the transition zone (TZ) and the peripheral zone (PZ)</p>
</div>
<p class="br"></p>
</div>
<p style="text-align:justify; font-size:18px">
- A goal of the Strand laboratory is to understand the cellular and
- molecular biology of lower urinary tract
- symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder
- dysfunction. BPH/LUTS is present in the
- vast majority of men over 70 years old resulting in medical
- treatment or surgical intervention.
+ A goal of the Strand laboratory is to understand the cellular and molecular biology of lower urinary tract
+ symptoms (LUTS) due to benign prostatic hyperplasia (BPH) or bladder dysfunction. BPH/LUTS is present in the
+ vast majority of men over 70 years old resulting in medical treatment or surgical intervention.
</p>
<p style="text-align:justify; font-size:18px">
- We focus on translational questions related to progression of
- BPH/LUTS in order to develop new targets for
- therapeutic intervention. In particular, we are interested in
- characterizing the cellular composition of
- particular phenotypes that are resistant to current therapies. We
- use a combination of single cell RNA
- sequencing, flow cytometry and immunohistochemistry on normal and
- diseased human specimens to build a
+ We focus on translational questions related to progression of BPH/LUTS in order to develop new targets for
+ therapeutic intervention. In particular, we are interested in characterizing the cellular composition of
+ particular phenotypes that are resistant to current therapies. We use a combination of single cell RNA
+ sequencing, flow cytometry and immunohistochemistry on normal and diseased human specimens to build a
cellular atlas of prostate and bladder disease.
</p>
</div>
@@ -84,82 +78,56 @@
<div class="section">
<H1 align="center">Pathological Heterogeneity in BPH</H1>
<div class="fig" style="max-width:500px">
- <img src="/research.images/pheno.jpg" alt="phenotypes" class="img"
- />
+ <img src="/research.images/pheno.jpg" alt="phenotypes" class="img" />
<div class="lab">
- <p>Phenotypic diversity in BPH. Left: glandular enlargement.
- Middle: Stromal enlargement. Right: Mixed
+ <p>Phenotypic diversity in BPH. Left: glandular enlargement. Middle: Stromal enlargement. Right: Mixed
type.</p>
</div>
</div>
<p style="text-align:justify; font-size:18px">
- We believe that the basis for heterogeneous clinical responses in
- BPH is pathologic diversity. There are a
- number of phenotypes evident across and even within patients. In one
- area, a patient can display a stromal
+ We believe that the basis for heterogeneous clinical responses in BPH is pathologic diversity. There are a
+ number of phenotypes evident across and even within patients. In one area, a patient can display a stromal
tumor while the other area display an epithelial nodule.
</p>
<p style="text-align:justify; font-size:18px">
- Our goal is to provide a rational basis for therapeutically treating
- these individual phenotypes by
- dissecting them macroscopically and then comparing their
- cell-specific molecular profiles to reduce the
- noise of cellular heterogeneity and inflammation. Our first goal is
- to identify a cell or cells of origin
- for the varying phenotypes by phenotyping the tissues with single
- cell RNA sequencing. This includes a
- comprehensive evaluation of the immune and inflammatory infiltrate
- as well as fluctuations in epithelial and
+ Our goal is to provide a rational basis for therapeutically treating these individual phenotypes by
+ dissecting them macroscopically and then comparing their cell-specific molecular profiles to reduce the
+ noise of cellular heterogeneity and inflammation. Our first goal is to identify a cell or cells of origin
+ for the varying phenotypes by phenotyping the tissues with single cell RNA sequencing. This includes a
+ comprehensive evaluation of the immune and inflammatory infiltrate as well as fluctuations in epithelial and
stromal subpopulations.
</p>
<p style="text-align:justify; font-size:18px">
- We are subsequently isolating the cell types of interest and
- performing molecular profiling. Based on these
- targets, we will use our mouse and cell culture models to
- experimentally test our hypotheses.
+ We are subsequently isolating the cell types of interest and performing molecular profiling. Based on these
+ targets, we will use our mouse and cell culture models to experimentally test our hypotheses.
</p>
</div>
<div class="section">
<H1 align="center">Clinical Heterogeneity in BPH</H1>
<p style="text-align:justify; font-size:18px">
- It is clear from clinical trials of medications for BPH that
- personalized therapies will be needed due to
- the highly variable responses. Typically, patients complaining of
- lower urinary tract symptoms are placed on
- an alpha-adrenergic receptor blocker as a first line therapy due to
- its fast-acting relief of symptoms.
- These drugs relieve smooth muscle tone and are most effective in
- patients with early stage disease
- displaying a high smooth muscle to epithelial tissue composition.
- However, as the prostate enlarges,
- epithelial nodules predominate the tissue decreasing the likelihood
- of alpha-blocker efficacy.
+ It is clear from clinical trials of medications for BPH that personalized therapies will be needed due to
+ the highly variable responses. Typically, patients complaining of lower urinary tract symptoms are placed on
+ an alpha-adrenergic receptor blocker as a first line therapy due to its fast-acting relief of symptoms.
+ These drugs relieve smooth muscle tone and are most effective in patients with early stage disease
+ displaying a high smooth muscle to epithelial tissue composition. However, as the prostate enlarges,
+ epithelial nodules predominate the tissue decreasing the likelihood of alpha-blocker efficacy.
</p>
<p style="text-align:justify; font-size:18px">
- The second-line therapy for BPH is a 5 alpha reductase inhibitor
- (5ARI), which induces epithelial apoptosis
- by decreasing the levels of intra-prostatic dihyrotestosterone
- (DHT). This therapy is effective at reducing
+ The second-line therapy for BPH is a 5 alpha reductase inhibitor (5ARI), which induces epithelial apoptosis
+ by decreasing the levels of intra-prostatic dihyrotestosterone (DHT). This therapy is effective at reducing
prostate size by 25 percent in most patients.
</p>
<p style="text-align:justify; font-size:18px">
- Importantly, either therapy only reduces symptomatic progression by
- 34 percent, suggesting
- androgen-independent mechanisms of prostate growth and symptoms need
- to be targeted. Responses to current
- drugs are further reduced in patients with obesity, diabetes, and
- dyslipidemia.
+ Importantly, either therapy only reduces symptomatic progression by 34 percent, suggesting
+ androgen-independent mechanisms of prostate growth and symptoms need to be targeted. Responses to current
+ drugs are further reduced in patients with obesity, diabetes, and dyslipidemia.
</p>
<p style="text-align:justify; font-size:18px">
- These data suggest that there are further measures that are
- necessary for every patient, and completely
- novel measures necessary for individual patients. Our goal is to
- characterize the cellular composition of
- particular phenotypes, and more deeply understand the molecular
- changes driving these phenotypes. We use a
- combination of single cell RNA sequencing, flow cytometry, and
- immunohistochemistry on specimens from young
+ These data suggest that there are further measures that are necessary for every patient, and completely
+ novel measures necessary for individual patients. Our goal is to characterize the cellular composition of
+ particular phenotypes, and more deeply understand the molecular changes driving these phenotypes. We use a
+ combination of single cell RNA sequencing, flow cytometry, and immunohistochemistry on specimens from young
organ donors and older men with prostatic enlargement.
</p>
</div>
diff --git a/layouts/custom/sc.data.html b/layouts/custom/sc.data.html
index 56052c0a592cab41a54cbc8bf23f93273ecf970e..604721f6637e9bf7a83b20493945613f49bafea5 100644
--- a/layouts/custom/sc.data.html
+++ b/layouts/custom/sc.data.html
@@ -1,14 +1,14 @@
{{ partial "header.html" . }}
<div class="header">
- <h1>{{ .Title }}</h1>
- <h2>{{ .Description }}</h2>
+ <h1>{{ .Title }}</h1>
+ <h2>{{ .Description }}</h2>
</div>
<div class="content">
- {{ range .Pages.ByWeight }}
+ {{ range .Pages.ByWeight }}
<li><a href="{{.Permalink}}">{{.Params.name}}</a></li>
- {{ end }}
+ {{ end }}
</div>
{{ partial "footer.html" . }}
\ No newline at end of file
diff --git a/static/css/.sidenavRepository.css.swn b/static/css/.sidenavRepository.css.swn
new file mode 100644
index 0000000000000000000000000000000000000000..283cf58f226274b32b2f4ac10f9e5eedba7890f1
Binary files /dev/null and b/static/css/.sidenavRepository.css.swn differ
diff --git a/static/css/.sidenavRepository.css.swo b/static/css/.sidenavRepository.css.swo
new file mode 100644
index 0000000000000000000000000000000000000000..111bbf3b415f4cb5398233b196fef68805cd6c44
Binary files /dev/null and b/static/css/.sidenavRepository.css.swo differ
diff --git a/static/css/.sidenavRepository.css.swp b/static/css/.sidenavRepository.css.swp
new file mode 100644
index 0000000000000000000000000000000000000000..1cc35e8d259bdfea2d591b0bdcbe48debfb56775
Binary files /dev/null and b/static/css/.sidenavRepository.css.swp differ
diff --git a/static/css/sidenavRepository.css b/static/css/sidenavRepository.css
new file mode 100644
index 0000000000000000000000000000000000000000..da06e06f809868c21a62ad5ebdcdc078d29ad4d5
--- /dev/null
+++ b/static/css/sidenavRepository.css
@@ -0,0 +1,59 @@
+/* the sidebar menu */
+.sidenav {
+ width: 30% ;
+ position: fixed/* stay in place on scroll */
+ /* z-index:1; /* stay on top*/
+ top : 0; /* stay on top*/
+ left: 0; /* on left side of screen */
+
+ background: #eee;
+ padding-top: 2px;
+ padding-right:2px;
+}
+
+/* Sidenav filters */
+.sidenav a, .dropdown-btn {
+ padding: 6px 6px 6px 6px;
+ text-decoration: none;
+ color: #818181;
+ display: block;
+ border: none;
+ background: none;
+ width:100%;
+ text-align: left;
+ cursor: pointer;
+ outline: none;
+}
+
+.numbers {
+ text-align: right;
+ padding: 0px 0px 0px 0px;
+ float: right;
+}
+
+#filter {
+ padding-left: 15px;
+ font-size: 85%;
+ clear: left;
+}
+
+
+/* On mouse-over */
+.sidenav a:hover, .dropdown-btn:hover {
+ color: #cacfd2 ;
+}
+
+
+/* Add an active class to the active dropdown button */
+.active {
+ background-color: #909497 ;
+ color: white;
+}
+
+/*change style of sidebar on smaller screens */
+@media screen and (max-height:450px){
+ .sidenav {padding-top: 15px;}
+ .sidenav a {font-size: 18px;}
+}
+
+
diff --git a/static/js/repoFilterLogic.js b/static/js/repoFilterLogic.js
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/static/js/repositoryJS.js b/static/js/repositoryJS.js
new file mode 100644
index 0000000000000000000000000000000000000000..93d263337f3507ac6206cbf1d26d0687931a23bc
--- /dev/null
+++ b/static/js/repositoryJS.js
@@ -0,0 +1,83 @@
+//$(document).ready(function(){
+
+
+//* Loop through all dropdown buttons to toggle between hiding and showing its dropdown content - This allows the user to have multiple dropdowns without any conflict */
+var dropdown = document.getElementsByClassName("dropdown-btn");
+var i;
+
+for (i = 0; i < dropdown.length; i++) {
+ dropdown[i].addEventListener("click", function() {
+ this.classList.toggle("active");
+ var dropdownContent = this.nextElementSibling;
+ if (dropdownContent.style.display === "block") {
+ dropdownContent.style.display = "none";
+ } else {
+ dropdownContent.style.display = "block";
+ }
+ });
+ }
+
+
+
+/* Get files matching filters
+
+//declare global vars
+ var results = []; //array of records that match the filters
+ var data = {{ index .Site.Data.scRNAseq_huPr_D.updated_cleaned_json }};
+ var numbers = $("#filter").find(".numbers"); //array of all the places we want to update with the # of records that match the filters
+ var filters = [];//array of current filters
+
+ //filtering function
+ $("input").click(function(){
+
+ // get specific vars
+ var name = $(this).attr("name");
+ var value = $(this).attr("value");
+ var id = name + value;
+ id= id.replace(/\s+/g, '');
+ var filterVar = {"name": name, "value":value, "id":id};
+
+ // if checkbox is checked: add filter values to filter
+ if ($(this).prop("checked") == true){
+ filters.push(filterVar);
+
+ /* var i;
+ for (i =0; i < data.length; i++){
+ if( data[i][name] == value){
+ results.push(data[i]);
+ $("#"+id).text[numbers.length];
+ }
+ }*/
+ /* }
+
+ //if checkbox is not checked: remove filter values from filter
+ else if ($(this).prop("checked") == false){
+ var i;
+ for (i=0; i<filter.length; i++){
+ if (filter[i][id]== id){
+ filter.splice(i, 1);
+ i--;
+ }
+ }
+ }
+
+ //check data to pull all records that match the current filters
+ var i;
+ var j;
+ for (i = 0; i<filters.length; i++){
+ var count = 0;
+ $('#displayFiles').text(numbers.length);
+
+ for (j=0; j <data.length; j++){
+ // var id2 = results[j][name]. + results[j][name];
+ // id2 = id2.replace(/\s+/g, '');
+ // $('#displayFiles').text(id2);
+ if (id2 == numbers[i][id]){
+ count++;
+ $('#displayFiles').text(count);
+ }
+ }
+ }
+ });
+});
+*/