tested v1.4.0

Author: wbaopaul

README.md

@@ -101,7 +101,7 @@ Dependencies
 -   trim\_galore (>=0.6.3), Trimmomatic (>=0.6.3)
 -   Regulratory Genomics Toolbox (RGT, for footprinting analysis)
 -   g++ compiler, bzip2, ncurses-devel
--   R packaages: devtools, flexdashboard, png, data.table, Matirx, Rcpp, ggplot2, flexmix, optparse, magrittr, readr, Seurat, bedr, gridExtra, ggrepel, kableExtra, viridis, xlsx, RColorBrewer,pheatmap,motifmatchr, chromVAR, chromVARmotifs, SummarizedExperiment, BiocParallel, DESeq2, clusterProfiler, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, VisCello.atac
+-   R packaages: devtools, flexdashboard, png, data.table, Matirx, Rcpp, ggplot2, flexmix, optparse, magrittr, readr, Seurat, bedr, gridExtra, ggrepel, kableExtra, viridis, xlsx, RColorBrewer,pheatmap,motifmatchr, chromVAR, chromVARmotifs, SummarizedExperiment, BiocParallel, DESeq2, clusterProfiler, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, VisCello.atac
 
 Quick start guide
 -----------

scripts/install/install_Rpackages.R

@@ -18,7 +18,7 @@ for(pk in pks){
 }
 
 bioc.pks = c('RColorBrewer','pheatmap','motifmatchr', 'chromVAR', 'SummarizedExperiment', 'BiocParallel', 'DESeq2', 'edgeR', 'matrixStats', 'cicero', 'farver', 'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10',  'clusterProfiler',
- 'DropletUtils')
+ 'DropletUtils', 'EnsDb.Hsapiens.v86', 'EnsDb.Mmusculus.v79')
 
 for(pk in bioc.pks){
     if(!require(pk, character.only = T)) {  

scripts/src/labelTransfer.R

@@ -15,7 +15,7 @@ gene_gtf_file = args[4]
 ## if gtf file not provided, using R bioconductor packages for gene annotation
 if(!file.exists(gene_gtf_file)){
   if(!grepl(GENOME_NAME, pattern = 'hg19|hg38|mm10|mm9', ignore.case = T)){
-    stop('Genome is not belong to hg19,hg38,mm9 and mm10, 
+    stop('Genome is not belong to any of hg19,hg38,mm9 or mm10, 
          please provide .gtf file for gene annotation!')
   }
   if(grepl(GENOME_NAME, pattern = 'mm10', ignore.case = T)) {