Update README.md

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)