metaseqR

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see metaseqR (see replacement metaseqR2).

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.


Bioconductor version: 3.9

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Author: Panagiotis Moulos <moulos at fleming.gr>

Maintainer: Panagiotis Moulos <moulos at fleming.gr>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("metaseqR")

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("metaseqR")
RNA-Seq data analysis using mulitple statistical algorithms with metaseqR PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, ReportWriting, Software, WorkflowStep
Version 1.24.0
In Bioconductor since BioC 2.14 (R-3.1) (10 years)
License GPL (>= 3)
Depends R (>= 2.13.0), EDASeq, DESeq, limma, qvalue
Imports edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots, corrplot, vsn, brew, rjson, log4r
System Requirements
URL http://www.fleming.gr
See More
Suggests BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite
Linking To
Enhances parallel, TCC, RMySQL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package metaseqR_1.24.0.tar.gz
Windows Binary metaseqR_1.24.0.zip
Mac OS X 10.11 (El Capitan) metaseqR_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/metaseqR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metaseqR
Bioc Package Browser https://code.bioconductor.org/browse/metaseqR/
Package Short Url https://bioconductor.org/packages/metaseqR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive