Commit 60f2d373 authored by Christian Arnold's avatar Christian Arnold

Version 1.1.4, see Changelog

parent f9c3995c
......@@ -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:
......
......@@ -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)
......
......@@ -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)
......
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