Last data update: 2014.03.03
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Ringo
Package: Ringo
Type: Package
Title: R Investigation of ChIP-chip Oligoarrays
Version: 1.36.0
Date: 2016-03-07
Author: Joern Toedling, Oleg Sklyar, Tammo Krueger, Matt Ritchie, Wolfgang Huber
Maintainer: J. Toedling <jtoedling@yahoo.de>
Depends: methods, Biobase (>= 1.14.1), RColorBrewer, limma, Matrix,
grid, lattice
Imports: BiocGenerics (>= 0.1.11), genefilter, limma, vsn, stats4
Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0)
Description: The package Ringo facilitates the primary analysis
of ChIP-chip data. The main functionalities of the package are
data read-in, quality assessment, data visualisation and
identification of genomic regions showing enrichment in ChIP-chip.
The package has functions to deal with two-color oligonucleotide
microarrays from NimbleGen used in ChIP-chip projects, but also
contains more general functions for ChIP-chip data analysis, given
that the data is supplied as RGList (raw) or ExpressionSet (pre-
processed).
The package employs functions from various other packages of the
Bioconductor project and provides additional ChIP-chip-specific
and NimbleGen-specific functionalities.
Reference: Joern Toedling, Oleg Sklyar, Tammo Krueger, Jenny J.
Fischer, Silke Sperling, and Wolfgang Huber (2007). Ringo - an
R/Bioconductor package for analyzing ChIP-chip readouts. BMC
Bioinformatics, 8:221.
License: Artistic-2.0
biocViews:
Microarray,TwoChannel,DataImport,QualityControl,Preprocessing
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2016-05-04 02:59:17 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'Ringo' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mmeansd.cpp -o mmeansd.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mmedian.cpp -o mmedian.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c region_overlap.c -o region_overlap.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ringo_init.c -o ringo_init.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/Ringo/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'ls' from package 'base' in package 'Ringo'
** help
*** installing help indices
converting help for package 'Ringo'
finding HTML links ... done
Ringo-internal html
arrayImage html
asExprSet html
autocorr html
cherByThreshold html
cherClass html
chipAlongChrom html
chipAlongChromOld html
computeRunningMedians html
compute_gc html
compute_sliding_t html
corrPlot html
exportCherList html
extractProbeAnno html
features2Probes html
findChersOnSmoothed html
ftr2xys html
getFeats html
newCER html
nimblegenNorm html
nonzero html
plotAutocorr html
plotBM html
plot_cher html
posToProbeAnnoEnvironment html
preprocess html
probeAnnoClass html
qopS4 html
quantilesOverPositions html
readNimblegen html
regionoverlap html
relateCERs html
sigGOTable html
sliding_meansd html
sliding_quantile html
twoGaussiansNull html
upperBoundNull html
validProbeAnno html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Ringo)
Making 'packages.html' ... done
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