TCC: TCC: Differential expression analysis for tag count data with robust normalization strategies

This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.

AuthorJianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji Kadota
Date of publicationNone
MaintainerJianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
LicenseGPL-2
Version1.14.0

View on Bioconductor

Functions

[ Man page
arab Man page
calcAUCValue Man page
calcNormFactors Man page
calcNormFactors,DGEList-method Man page
calcNormFactors,TCC-method Man page
clusterSample Man page
estimateDE Man page
filterLowCountGenes Man page
getNormalizedData Man page
getResult Man page
hypoData Man page
hypoData_mg Man page
hypoData_ts Man page
length Man page
length,TCC-method Man page
makeFCMatrix Man page
nakai Man page
names Man page
names,TCC-method Man page
plot Man page
plotFCPseudocolor Man page
plot.TCC Man page
ROKU Man page
show Man page
show.TCC Man page
show,TCC-method Man page
simulateReadCounts Man page
subset Man page
subset,TCC-method Man page
TCC Man page
[,TCC,ANY,ANY,ANY-method Man page
[,TCC,ANY,ANY-method Man page
[,TCC,ANY-method Man page
TCC-class Man page
[,TCC-method Man page
TCC-package Man page
WAD Man page

Files

TCC/DESCRIPTION
TCC/NAMESPACE
TCC/NEWS
TCC/R
TCC/R/ROKU.R TCC/R/TCC.R TCC/R/TCC.calcNormFactors.R TCC/R/TCC.estimateDE.DESeq.R TCC/R/TCC.estimateDE.DESeq2.R TCC/R/TCC.estimateDE.R TCC/R/TCC.estimateDE.SAMseq.R TCC/R/TCC.estimateDE.WAD.R TCC/R/TCC.estimateDE.YAYOI.R TCC/R/TCC.estimateDE.baySeq.R TCC/R/TCC.estimateDE.edgeR.R TCC/R/TCC.estimateDE.limmavoom.R TCC/R/TCC.generic.R TCC/R/TCC.getNormalizedData.R TCC/R/TCC.plotMA.R TCC/R/TCC.public.R TCC/R/TCC.simulation.R TCC/R/TCC_0.4.R TCC/R/WAD.R TCC/R/YAYOI.R TCC/R/clusterSample.R
TCC/build
TCC/build/vignette.rds
TCC/data
TCC/data/arab.RData
TCC/data/hypoData.RData
TCC/data/hypoData_mg.RData
TCC/data/hypoData_ts.RData
TCC/data/nakai.RData
TCC/inst
TCC/inst/CITATION
TCC/inst/doc
TCC/inst/doc/TCC.R
TCC/inst/doc/TCC.Rnw
TCC/inst/doc/TCC.pdf
TCC/inst/unitTests
TCC/inst/unitTests/test_ROKU.R
TCC/inst/unitTests/test_WAD.R
TCC/inst/unitTests/test_calcNormFactors.R
TCC/inst/unitTests/test_clusterSample.R
TCC/inst/unitTests/test_estimateDE.R
TCC/inst/unitTests/test_getResult.R
TCC/inst/unitTests/test_new.R
TCC/inst/unitTests/test_plot.R
TCC/inst/unitTests/test_plotFCPseudocolor.R
TCC/man
TCC/man/ROKU.Rd TCC/man/TCC-class.Rd TCC/man/TCC.Rd TCC/man/WAD.Rd TCC/man/arab.Rd TCC/man/calcAUCValue.Rd TCC/man/calcNormFactors.Rd TCC/man/clusterSample.Rd TCC/man/estimateDE.Rd TCC/man/filterLowCountGenes.Rd TCC/man/getNormalizedData.Rd TCC/man/getResult.Rd TCC/man/hypoData.Rd TCC/man/hypoData_mg.Rd TCC/man/hypoData_ts.Rd TCC/man/makeFCMatrix.Rd TCC/man/nakai.Rd TCC/man/plot.TCC.Rd TCC/man/plotFCPseudocolor.Rd TCC/man/simulateReadCounts.Rd
TCC/tests
TCC/tests/runTests.R
TCC/vignettes
TCC/vignettes/TCC.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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