get ready for testing

bcbio · Jul 26, 2024 · 6e5d610 · 6e5d610
1 parent fe38272
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diff --git a/inst/templates/singlecell/CellToCell/cellchat.Rmd b/inst/templates/singlecell/CellToCell/cellchat.Rmd
@@ -437,4 +437,4 @@ gg1 <- netVisual_bubble(cellchat_merged,
                         angle.x = 45, 
                         remove.isolate = T)
 gg1
-signaling.grade2_increased = gg1$data
+signaling.grade2_increased = gg1$data
diff --git a/...emplates/singlecell/scRNA_qc_template.rmd → inst/templates/singlecell/QC.rmd b/...emplates/singlecell/scRNA_qc_template.rmd → inst/templates/singlecell/QC.rmd
diff --git a/inst/templates/singlecell/README.md b/inst/templates/singlecell/README.md
@@ -3,3 +3,19 @@
 # Start with cell-ranger
 
 `pre-process-w-cellranger.md` contains step by step guidelines on how to run cellranger in O2 and load data into R. This `scripts/seurat_init.R` script contains all the pieces to go from cellranger output to Seurat obj. It is assuming a mouse genome.
+
+# QC
+
+Currently we are working on deploying a shiny app to inspect the single cell object and find the best cut-offs for filtering. The Rmd that helps to visualize the before and after is `QC.Rmd`.
+
+# Integration
+
+Currently we are working on guidelines and templates for this step. There is some draft under *Integration** folder.
+
+# Cell to cell communication
+
+CellChat template is at `CellToCell/cellchat.Rmd`. We have built a stable environment in O2 using the following modules:
+
+```
+# gcc/9.2.0 imageMagick/7.1.0 geos/3.10.2 cmake/3.22.2 R/4.3.1 fftw/3.3.10 gdal/3.1.4 udunits/2.2.28  boost/1.75.0 python/3.9.14
+```