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Commit ac554efd authored by Spencer Barnes's avatar Spencer Barnes
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adding version 1

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README.md
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...@@ -2,36 +2,36 @@ Author: Min Kim <MinS.Kim@UTSouthwestern.edu> and Spencer Barnes <Spencer.Barnes ...@@ -2,36 +2,36 @@ Author: Min Kim <MinS.Kim@UTSouthwestern.edu> and Spencer Barnes <Spencer.Barnes
Date: April 20, 2017 Date: April 20, 2017
Description: Shiny app for analyzing TCGA data for frequently asked requests through the Help-Desk. Description: Shiny app for analyzing TCGA data for frequently asked requests through the Help-Desk.
Project name Cancer type Project name Cancer type
ACC Adrenocortical Carcinoma ACC Adrenocortical Carcinoma
BLCA Bladder Urothelial Carcinoma BLCA Bladder Urothelial Carcinoma
BRCA Breast Invasive Carcinoma BRCA Breast Invasive Carcinoma
CESC Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma CESC Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
CHOL Cholangiocarcinoma CHOL Cholangiocarcinoma
COAD Colon Adenocarcinoma COAD Colon Adenocarcinoma
DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
GBM Glioblastoma Multiforme GBM Glioblastoma Multiforme
HNSC Head and Neck Squamous Cell Carcinoma HNSC Head and Neck Squamous Cell Carcinoma
KICH Kidney Chromophobe KICH Kidney Chromophobe
KIRC Kidney Renal Clear Cell Carcinoma KIRC Kidney Renal Clear Cell Carcinoma
KIRP Kidney Renal Papillary Cell Carcinoma KIRP Kidney Renal Papillary Cell Carcinoma
LAML Acute Myeloid Leukemia LAML Acute Myeloid Leukemia
LGG Brain Lower Grade Glioma LGG Brain Lower Grade Glioma
LIHC Liver Hepatocellular Carcinoma LIHC Liver Hepatocellular Carcinoma
LUAD Lung Adenocarcinoma LUAD Lung Adenocarcinoma
LUSC Lung Squamous Cell Carcinoma LUSC Lung Squamous Cell Carcinoma
MESO Mesothelioma MESO Mesothelioma
OV Ovarian Serous Cystadenocarcinoma OV Ovarian Serous Cystadenocarcinoma
PAAD Pancreatic Adenocarcinoma PAAD Pancreatic Adenocarcinoma
PCPG Pheochromocytoma and Paraganglioma PCPG Pheochromocytoma and Paraganglioma
PRAD Prostate Adenocarcinoma PRAD Prostate Adenocarcinoma
READ Rectum Adenocarcinoma READ Rectum Adenocarcinoma
SARC Sarcoma SARC Sarcoma
SKCM Skin Cutaneous Melanoma SKCM Skin Cutaneous Melanoma
TGCT Testicular Germ Cell Tumors TGCT Testicular Germ Cell Tumors
THCA Thyroid Carcinoma THCA Thyroid Carcinoma
THYM Thymoma THYM Thymoma
UCEC Uterine Corpus Endometrial Carcinoma UCEC Uterine Corpus Endometrial Carcinoma
UCS Uterine Carcinosarcoma UCS Uterine Carcinosarcoma
UVM Uveal Melanoma UVM Uveal Melanoma
scripts/server.R 100755 → 100644
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scripts/tcga_genes.txt 0 → 100755
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scripts/ui.R 100755 → 100644
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shinyUI( shinyUI(
pageWithSidebar( fluidPage(
headerPanel("TGCA Analysis"), headerPanel("TCGA Analysis"),
sidebarPanel( sidebarLayout(
selectInput("operation","Select Plot Type",choices = c("Pancan","Survival")), sidebarPanel(
conditionalPanel(condition = "input.operation=='Pancan'", selectInput("operation","Select Plot Type",choices = c("Boxplot","Survival")),
selectInput("cancerType","Select one or more cancer types", conditionalPanel(condition = "input.operation=='Boxplot'",
choices = substr(list.files("../Expression/",pattern=".txt"),1, selectInput("cancerType","Select one or more cancer types",
nchar(list.files("../Expression/",pattern=".txt"))-4), choices = substr(list.files("../Expression/",pattern=".txt"),1,
multiple = TRUE), nchar(list.files("../Expression/",pattern=".txt"))-4),
textInput("gene","Please input one gene of interest",placeholder = "Gene name ie 'TRIM21'") multiple = TRUE),
), textInput("gene","Please input one gene of interest",placeholder = "Gene name ie TRIM21")
conditionalPanel(condition="input.operation=='Survival'", ),
selectInput("cancerType2","Select a cancer type", conditionalPanel(condition="input.operation=='Survival'",
choices = substr(list.files("../Expression/",pattern=".txt"),1, selectInput("cancerType2","Select a cancer type",
nchar(list.files("../Expression/",pattern=".txt"))-4)), choices = substr(list.files("../Expression/",pattern=".txt"),1,
textInput("gene2","Please input one gene of interest",placeholder = "Gene name ie 'TRIM21'",value="TRIM21"), nchar(list.files("../Expression/",pattern=".txt"))-4)),
sliderInput("cut.off","Select a cutoff value",min = .10,max=.50,step = .05,value = .25) textInput("gene2","Please input one gene of interest",placeholder = "Gene name ie BRCA1"),
selectInput("operation2","Select automatic or manual cutoff", choices = c("Automatic", "Manual"))
),
conditionalPanel(condition="input.operation2=='Manual' & input.operation=='Survival'",
sliderInput("cut.off","Select a cutoff value",min = .10,max=.50,step = .05,value = .25)
),
actionButton("go","GO")
), ),
actionButton("go","GO") mainPanel(
#conditionalPanel(condition = "input.operation=='Pancan'" plotOutput("myPlot"),
downloadButton('downloadplot',"Download Figure")
# ) )
#selectInput("Distribution", "Select dist type",
# choices=c("normal","expo")),
#sliderInput("sampleSize","Select sample size: ",
# min=100,max=5000,value=1000,step=100),
#conditionalPanel(condition = "input.Distribution=='normal'",
# textInput("Mean","Plase Select the mean",10),
# textInput("sd","Please Select Standard Deviation",3)),
#conditionalPanel(condition="input.Distribution == 'expo'",
# textInput("lambda","Pleas select Expo Lambda",1)
#)
),
mainPanel(
plotOutput("myPlot")
) )
) )
) )
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