Last data update: 2014.03.03
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edgeR
Package: edgeR
Version: 3.14.0
Date: 2016-04-19
Title: Empirical Analysis of Digital Gene Expression Data in R
Description: Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.
Author: Yunshun Chen <yuchen@wehi.edu.au>, Aaron Lun <alun@wehi.edu.au>, Davis McCarthy <dmccarthy@wehi.edu.au>, Xiaobei Zhou <xiaobei.zhou@uzh.ch>, Mark Robinson <mark.robinson@imls.uzh.ch>, Gordon Smyth <smyth@wehi.edu.au>
Maintainer: Yunshun Chen <yuchen@wehi.edu.au>, Aaron Lun <alun@wehi.edu.au>, Mark Robinson <mark.robinson@imls.uzh.ch>, Davis McCarthy <dmccarthy@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
License: GPL (>=2)
Depends: R (>= 2.15.0), limma
Imports: graphics, stats, utils, methods
Suggests: MASS, statmod, splines, locfit, KernSmooth
URL: http://bioinf.wehi.edu.au/edgeR
biocViews: GeneExpression, Transcription, AlternativeSplicing,
Coverage, DifferentialExpression, DifferentialSplicing,
GeneSetEnrichment, Genetics, Bayesian, Clustering, Regression,
TimeCourse, SAGE, Sequencing, ChIPSeq, RNASeq, BatchEffect,
MultipleComparison, Normalization, QualityControl
NeedsCompilation: yes
Packaged: 2016-05-04 03:09:43 UTC; biocbuild
● BiocViews: AlternativeSplicing, BatchEffect, Bayesian, ChIPSeq, Clustering, Coverage, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, Genetics, MultipleComparison, Normalization, QualityControl, RNASeq, Regression, SAGE, Sequencing, TimeCourse, Transcription
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19 images,
83 functions,
0 datasets
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Reverse Depends: 13
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'edgeR' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_compute_nbdev.cpp -o R_compute_nbdev.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_cr_adjust.cpp -o R_cr_adjust.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_exact_test_by_deviance.cpp -o R_exact_test_by_deviance.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_levenberg.cpp -o R_levenberg.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_loess_by_col.cpp -o R_loess_by_col.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_maximize_interpolant.cpp -o R_maximize_interpolant.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_one_group.cpp -o R_one_group.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_process_hairpin_reads.c -o R_process_hairpin_reads.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_simple_good_turing.cpp -o R_simple_good_turing.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c adj_coxreid.cpp -o adj_coxreid.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c fmm_spline.c -o fmm_spline.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c glm_levenberg.cpp -o glm_levenberg.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c glm_one_group.cpp -o glm_one_group.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.cpp -o init.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c interpolator.cpp -o interpolator.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c matvec_check.cpp -o matvec_check.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c nbdev.cpp -o nbdev.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o edgeR.so R_compute_nbdev.o R_cr_adjust.o R_exact_test_by_deviance.o R_levenberg.o R_loess_by_col.o R_maximize_interpolant.o R_one_group.o R_process_hairpin_reads.o R_simple_good_turing.o adj_coxreid.o fmm_spline.o glm_levenberg.o glm_one_group.o init.o interpolator.o matvec_check.o nbdev.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/edgeR/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'edgeR'
finding HTML links ... done
DGEExact-class html
DGEGLM-class html
DGELRT-class html
DGEList-class html
DGEList html
WLEB html
adjustedProfileLik html
asdataframe html
asmatrix html
Rd warning: /tmp/RtmpWCS3Sy/R.INSTALL60fc42babaab/edgeR/man/asmatrix.Rd:24: missing file link 'as.matrix.RGList'
aveLogCPM html
binomTest html
calcNormFactors html
camera.DGEList html
finding level-2 HTML links ... done
commonCondLogLikDerDelta html
condLogLikDerSize html
cpm html
cutWithMinN html
decidetestsDGE html
dglmStdResid html
diffSpliceDGE html
dim html
dimnames html
dispBinTrend html
dispCoxReid html
dispCoxReidInterpolateTagwise html
dispCoxReidSplineTrend html
dropEmptyLevels html
edgeR-package html
edgeRUsersGuide html
equalizeLibSizes html
estimateCommonDisp html
estimateDisp html
estimateExonGenewisedisp html
estimateGLMCommonDisp html
estimateGLMRobustDisp html
estimateGLMTagwiseDisp html
estimateGLMTrendedDisp html
estimateTagwiseDisp html
estimateTrendedDisp html
exactTest html
expandAsMatrix html
getCounts html
getPriorN html
gini html
glmQLFTest html
glmTreat html
glmfit html
goana html
gof html
goodTuring html
loessByCol html
maPlot html
maximizeInterpolant html
maximizeQuadratic html
meanvar html
mglm html
movingAverageByCol html
nbinomDeviance html
normalizeChIPtoInput html
plotBCV html
plotExonUsage html
plotMD html
plotMDS.DGEList html
plotQLDisp html
plotSmear html
plotSpliceDGE html
predFC html
processAmplicons html
q2qnbinom html
readDGE html
roast.DGEList html
romer.DGEList html
spliceVariants html
splitIntoGroups html
subsetting html
sumTechReps html
systematicSubset html
thinCounts html
topSpliceDGE html
topTags html
validDGEList html
weightedCondLogLikDerDelta html
zscoreNBinom html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (edgeR)
Making 'packages.html' ... done
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