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

Files in this package

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

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