TCC
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see TCC.
TCC: Differential expression analysis for tag count data with robust normalization strategies
Bioconductor version: 3.11
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 <wukong at bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin at staff.kanazawa-u.ac.jp>
citation("TCC")):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.0), methods, DESeq, DESeq2, edgeR, baySeq, ROC |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | RUnit, BiocGenerics |
| Linking To | |
| Enhances | snow |
| Depends On Me | |
| Imports Me | |
| Suggests Me | compcodeR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TCC_1.28.0.tar.gz |
| Windows Binary | TCC_1.28.0.zip |
| macOS 10.13 (High Sierra) | TCC_1.28.0.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 |
| Old Source Packages for BioC 3.11 | Source Archive |