TCC: TCC: Differential expression analysis for tag count data with robust normalization strategies
Version 1.16.0

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
Bioconductor views DifferentialExpression RNASeq Sequencing
Date of publicationNone
MaintainerJianqiang Sun <wukong@bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
LicenseGPL-2
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("TCC")

Popular man pages

calcAUCValue: Calculate AUC value from a TCC-class object
calcNormFactors: Calculate normalization factors
filterLowCountGenes: Filter genes from a TCC-class object
hypoData: A simulation dataset for comparing two-group tag count data,...
plot.TCC: Plot a log fold-change versus log average expression...
ROKU: detect tissue-specific (or tissue-selective) patterns from...
TCC: A package for differential expression analysis from tag count...
See all...

All man pages Function index File listing

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

Functions

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ROKU.R
R/TCC.R
R/TCC.calcNormFactors.R
R/TCC.estimateDE.DESeq.R
R/TCC.estimateDE.DESeq2.R
R/TCC.estimateDE.R
R/TCC.estimateDE.SAMseq.R
R/TCC.estimateDE.WAD.R
R/TCC.estimateDE.YAYOI.R
R/TCC.estimateDE.baySeq.R
R/TCC.estimateDE.edgeR.R
R/TCC.estimateDE.limmavoom.R
R/TCC.generic.R
R/TCC.getNormalizedData.R
R/TCC.plotMA.R
R/TCC.public.R
R/TCC.simulation.R
R/TCC_0.4.R
R/WAD.R
R/YAYOI.R
R/clusterSample.R
build
build/vignette.rds
data
data/arab.RData
data/hypoData.RData
data/hypoData_mg.RData
data/hypoData_ts.RData
data/nakai.RData
inst
inst/CITATION
inst/doc
inst/doc/TCC.R
inst/doc/TCC.Rnw
inst/doc/TCC.pdf
inst/unitTests
inst/unitTests/test_ROKU.R
inst/unitTests/test_WAD.R
inst/unitTests/test_calcNormFactors.R
inst/unitTests/test_clusterSample.R
inst/unitTests/test_estimateDE.R
inst/unitTests/test_getResult.R
inst/unitTests/test_new.R
inst/unitTests/test_plot.R
inst/unitTests/test_plotFCPseudocolor.R
man
man/ROKU.Rd
man/TCC-class.Rd
man/TCC.Rd
man/WAD.Rd
man/arab.Rd
man/calcAUCValue.Rd
man/calcNormFactors.Rd
man/clusterSample.Rd
man/estimateDE.Rd
man/filterLowCountGenes.Rd
man/getNormalizedData.Rd
man/getResult.Rd
man/hypoData.Rd
man/hypoData_mg.Rd
man/hypoData_ts.Rd
man/makeFCMatrix.Rd
man/nakai.Rd
man/plot.TCC.Rd
man/plotFCPseudocolor.Rd
man/simulateReadCounts.Rd
tests
tests/runTests.R
vignettes
vignettes/TCC.Rnw
TCC documentation built on May 20, 2017, 9:31 p.m.

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