Version 1.1.4, see Changelog

VERSION

-1.1.3
+1.1.4

docs/chapter1.rst

@@ -98,10 +98,10 @@ A working ``R`` installation is needed and a number of packages from either CRAN
 
 .. code-block:: R
 
-  install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "RColorBrewer", "ggrepel", "lsr", "modeest", "boot", "grDevices", "pheatmap", "matrixStats", "locfdr"))
+  install.packages(c("checkmate", "futile.logger", "tidyverse", "reshape2", "RColorBrewer", "ggrepel", "lsr", "modeest", "boot", "grDevices", "pheatmap", "matrixStats", "locfdr", "pheatmap"))
   source("https://bioconductor.org/biocLite.R")
   biocLite(c("limma", "vsn", "csaw", "DESeq2", "DiffBind", "geneplotter", "Rsamtools"))
- 
+
 
 .. _docs-runOwnAnalysis:
 

docs/projectInfo.rst

@@ -31,6 +31,9 @@ We also put the paper on *bioRxiv*, please read all methodological details here:
 Change log
 ============================
 
+Version 1.1.4 (2018-08-09)
+    - minor, updated the checkParameterValidity.R script and the documentation (one package was not mentioned)
+
 Version 1.1.3 (2018-08-06)
     - minor, fixed a small issue in the Volcano plot (legends wrong and background color in the plot was not colored properly)
 

src/R/checkParameterValidity.R

@@ -86,23 +86,23 @@ printParametersLog(par.l)
 # LOAD ALL LIBRARIES #
 ######################
 
-# Step 1
+# createConsensusPeaks.R
 checkAndLoadPackages(c("tidyverse", "futile.logger", "DiffBind", "checkmate", "stats"), verbose = FALSE)
 
-# Step 2
-checkAndLoadPackages(c("tidyverse", "futile.logger", "DESeq2", "vsn", "csaw", "checkmate", "limma", "tools", "geneplotter", "RColorBrewer"), verbose = FALSE)
+# diffPeaks.R
+checkAndLoadPackages(c("tidyverse", "futile.logger", "DESeq2", "csaw", "checkmate", "limma", "tools"), verbose = FALSE)
 
-# Step 3
+# analyzeTF.R
 checkAndLoadPackages(c("tidyverse", "futile.logger", "DESeq2", "vsn", "modeest", "checkmate", "limma", "geneplotter", "RColorBrewer", "tools"), verbose = FALSE)
 
-# Step 4
+# summary1.R
 checkAndLoadPackages(c("tidyverse", "futile.logger", "modeest", "checkmate", "ggrepel"), verbose = FALSE)
 
-# Step 5
-checkAndLoadPackages(c("tidyverse", "futile.logger", "checkmate", "tools", "methods", "boot"), verbose = FALSE)
+# binningTF.R
+checkAndLoadPackages(c("tidyverse", "futile.logger", "lsr", "ggrepel", "checkmate", "tools", "methods", "boot"), verbose = FALSE)
 
-# Step 6
-checkAndLoadPackages(c("tidyverse", "futile.logger", "lsr", "ggrepel", "checkmate", "tools", "methods", "grDevices", "pheatmap"), verbose = TRUE)
+# summaryFinal.R
+checkAndLoadPackages(c("tidyverse", "futile.logger", "lsr", "DESeq2",  "matrixStats", "ggrepel", "checkmate", "tools", "grDevices", "locfdr", "pheatmap"), verbose = FALSE)