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Zaugg Group
diffTF
Commits
60f2d373
Commit
60f2d373
authored
Aug 09, 2018
by
Christian Arnold
Browse files
Version 1.1.4, see Changelog
parent
f9c3995c
Changes
4
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VERSION
View file @
60f2d373
1.1.
3
1.1.
4
docs/chapter1.rst
View file @
60f2d373
...
...
@@ -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:
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docs/projectInfo.rst
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60f2d373
...
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@@ -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)
...
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src/R/checkParameterValidity.R
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60f2d373
...
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@@ -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
=
TRU
E
)
#
summaryFinal.R
checkAndLoadPackages
(
c
(
"tidyverse"
,
"futile.logger"
,
"lsr"
,
"DESeq2"
,
"matrixStats"
,
"ggrepel"
,
"checkmate"
,
"tools"
,
"
grDevices"
,
"locfdr
"
,
"pheatmap"
),
verbose
=
FALS
E
)
...
...
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