From 95cafb6fa6b4182106e613662b9a1c36158838d5 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 6 Aug 2018 10:40:19 -0500
Subject: [PATCH] Update README.md
---
README.md | 28 +++++++++++++++++++++++-----
1 file changed, 23 insertions(+), 5 deletions(-)
diff --git a/README.md b/README.md
index 1e1b486..b36447b 100755
--- a/README.md
+++ b/README.md
@@ -15,6 +15,22 @@ Data Analysis
-------------
* **Requirements:**
+ * /analysis/DATA/D17PrF/
+ * D17PrF-demultiplex.csv
+ * 10x/
+ * aggregation_csv.csv
+ * GRCh38/
+ * "barcodes.tsv"
+ * "genes.tsv"
+ * "matrix.mtx"
+ * /analysis/DATA/D27PrF/
+ * D27PrF-demultiplex.csv
+ * 10x/
+ * aggregation_csv.csv
+ * GRCh38/
+ * "barcodes.tsv"
+ * "genes.tsv"
+ * "matrix.mtx"
* 10x CellRanger analyzed data:
* "filtered\_gene\_bc\_matrice_mex" folder
* csv file cellranger aggr used for aggregation
@@ -28,8 +44,14 @@ Data Analysis
* pastecs (v1.3.21)
* qusage (v2.10.0)
* RColorBrewer (v1.1-2)
+ * monocle (v2.6.3)
+ * dplyr (v0.7.6)
* *and all dependencies*
-
+* **HOW TO RUN**
+ * 1 Patient D17PrF
+ * run bash script sc_TissueMapper-D17PrF.sh
+ * 2 Patients D17PrF and D27PrF
+ * run bash script sc_TissueMapper-DPrF2.sh
* **Pipeline:**
* Link cellranger count/aggr output to analysis
* Create demultiplex file to add custom sample groups
@@ -77,10 +99,6 @@ Data Analysis
* "genes.deg.LE.csv" DWS generated DEGs of luminal epithelial cells from scRNA-Seq of patient D17 only
* "genes.deg.OE1.csv" DWS generated DEGs of "other" epithelia cluster 1 cells from scRNA-Seq of patient D17 only
* "genes.deg.OE2.csv" DWS generated DEGs of "other" epithelia cluster 2 cells from scRNA-Seq of patient D17 only
- * "" DWS generated DEGs of basal epithelial cells from scRNA-Seq of an aggregation of patient D17 and D27
- * "" DWS generated DEGs of luminal epithelial cells from scRNA-Seq of an aggregation of patient D17 and D27
- * "" DWS generated DEGs of "other" epithelia cluster 1 cells from scRNA-Seq of an aggregation of patient D17 and D27
- * "" DWS generated DEGs of "other" epithelia cluster 2 cells from scRNA-Seq of an aggregation of patient D17 and D27
* Stroma:
* "DEG\_C5.BP.M11704.txt" MSigDB C5 GO Biological Processes M11704 [**GO\_ENDOTHELIAL\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_ENDOTHELIAL_CELL_DIFFERENTIATION.html)
* "DEG\_C5.BP.M10794.txt" MSigDB C5 GO Biological Processes M10794 [**GO\_SMOOTH\_MUSCLE\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_SMOOTH_MUSCLE_CELL_DIFFERENTIATION.html)
--
GitLab