tweaked bin-paths

dge_workflow/dge_utils.sh

@@ -5,11 +5,11 @@
 #source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/bash/lsf_utils.sh 2>&1 2>/dev/null)
 
 ## enable snippet spinning
-source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
-export PATH=/home/brandl/bin/spinr:$PATH
+source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.22/R/spinr/spin_utils.sh 2>&1 2>/dev/null)
+export PATH=/projects/bioinfo/holger/bin//spinr:$PATH
 
 source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.20/R/rendr/rendr_utils.sh 2>&1 2>/dev/null)
-export PATH=/home/brandl/bin/rendr:$PATH
+export PATH=/projects/bioinfo/holger/bin//rendr:$PATH
 
 
 ## define common binaries
@@ -18,7 +18,7 @@ export PATH=/projects/bioinfo/holger/bin/bowtie2-2.2.5:$PATH
 export PATH=/projects/bioinfo/holger/bin/tophat-2.0.13.Linux_x86_64:$PATH
 export PATH=/home/brandl/bin/cufflinks-2.2.1.Linux_x86_64:$PATH
 export PATH=/sw/apps/python/current/bin:$PATH
-export PATH=/home/brandl/bin/deepTools/bin:$PATH
+export PATH=/projects/bioinfo/holger/bin/deepTools/bin:$PATH
 export PATH=/projects/bioinfo/holger/bin/FastQC_0.11.2:$PATH
 export PATH=/projects/bioinfo/holger/bin/bedtools2-2.25.0/bin/:$PATH
 export PATH=/projects/bioinfo/holger/bin/samtools-1.3:$PATH

dge_workflow/featcounts_deseq.R

@@ -126,8 +126,8 @@ if(!all((contrasts %>% gather %$% value %>% unique) %in% colData$condition)){
 #stopifnot(all((contrasts %>% gather %$% value %>% unique) %in% colData$condition))
 
 dds <- DESeqDataSetFromMatrix(countMatrix, colData, formula(~ condition))
-dds <- estimateSizeFactors(dds)
-dds <- estimateDispersions(dds)
+#dds <- estimateSizeFactors(dds)
+#dds <- estimateDispersions(dds)
 
 
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