metaseqR

DOI: 10.18129/B9.bioc.metaseqR    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DifferentialExpression, GeneExpression, ImmunoOncology, Normalization, Preprocessing, QualityControl, RNASeq, ReportWriting, Software, WorkflowStep
Version	1.30.0
In Bioconductor since	BioC 2.14 (R-3.1) (7 years)
License	GPL (>= 3)
Depends	R (>= 3.4.0), EDASeq, DESeq, limma, qvalue
Imports	edgeR, NOISeq, baySeq, NBPSeq, biomaRt, utils, gplots, corrplot, vsn, brew, rjson, log4r
LinkingTo
Suggests	BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite
SystemRequirements
Enhances	parallel, TCC, RMySQL
URL	http://www.fleming.gr
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	metaseqR_1.30.0.tar.gz
Windows Binary	metaseqR_1.30.0.zip
macOS 10.13 (High Sierra)	metaseqR_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/metaseqR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/metaseqR
Package Short Url	https://bioconductor.org/packages/metaseqR/
Package Downloads Report	Download Stats