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

Share:

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.

Author
Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, and Koji Kadota
Date of publication
None
Maintainer
Jianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
License
GPL-2
Version
1.14.0

View on Bioconductor

Man pages

arab
Arabidopsis RNA-Seq data set
calcAUCValue
Calculate AUC value from a TCC-class object
calcNormFactors
Calculate normalization factors
clusterSample
Perform hierarchical clustering for samples from expression...
estimateDE
Estimate degrees of differential expression (DE) for...
filterLowCountGenes
Filter genes from a TCC-class object
getNormalizedData
Obtain normalized count data
getResult
Obtain the summaries of results after the differential...
hypoData
A simulation dataset for comparing two-group tag count data,...
hypoData_mg
A simulation dataset for comparing three-group tag count...
hypoData_ts
A sample microarray data for detecting tissue-specific...
makeFCMatrix
Generate the fold change matrix for simulating count data
nakai
DNA microarray data set
plotFCPseudocolor
Create a pseudo-color image of simulation data
plot.TCC
Plot a log fold-change versus log average expression...
ROKU
detect tissue-specific (or tissue-selective) patterns from...
simulateReadCounts
Generate simulation data from negative binomial (NB)...
TCC
A package for differential expression analysis from tag count...
TCC-class
A container for storing information used in TCC
WAD
Calculate WAD statistic for individual genes

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