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TCC

This is the development version of TCC; for the stable release version, see TCC.

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


Bioconductor version: Development (3.19)

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

Maintainer: Jianqiang Sun <sun at biunit.dev>, Tomoaki Nishiyama <tomoakin at staff.kanazawa-u.ac.jp>

Citation (from within R, enter citation("TCC")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TCC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TCC")
TCC PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.43.4
In Bioconductor since BioC 2.13 (R-3.0) (10.5 years)
License GPL-2
Depends R (>= 3.0), methods, DESeq2, edgeR, ROC
Imports
System Requirements
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Suggests RUnit, BiocGenerics
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Depends On Me
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Suggests Me compcodeR
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TCC_1.43.4.tar.gz
Windows Binary TCC_1.43.4.zip
macOS Binary (x86_64) TCC_1.43.4.tgz
macOS Binary (arm64) TCC_1.43.4.tgz
Source Repository git clone https://git.bioconductor.org/packages/TCC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TCC
Bioc Package Browser https://code.bioconductor.org/browse/TCC/
Package Short Url https://bioconductor.org/packages/TCC/
Package Downloads Report Download Stats