metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see metaseqR2.

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

Bioconductor version: 3.17

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 [aut, cre]

Maintainer: Panagiotis Moulos <moulos at fleming.gr>

Citation (from within R, enter citation("metaseqR2")):

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("metaseqR2")

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

Documentation

PDF   Reference Manual

Details

biocViews ATACSeq, AlternativeSplicing, BatchEffect, Bayesian, BiomedicalInformatics, CellBiology, ChIPSeq, Clustering, DataImport, DifferentialExpression, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, ImmunoOncology, MultipleComparison, Normalization, Preprocessing, ProprietaryPlatforms, QualityControl, RNASeq, Regression, ReportWriting, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics, WorkflowStep
Version 1.12.0
In Bioconductor since BioC 3.11 (R-4.0) (3.5 years)
License GPL (>= 3)
Depends R (>= 4.0.0), DESeq2, limma, locfit, splines
Imports ABSSeq, baySeq, Biobase, BiocGenerics, BiocParallel, biomaRt, Biostrings, corrplot, DSS, DT, EDASeq, edgeR, genefilter, GenomeInfoDb, GenomicAlignments, GenomicFeatures, GenomicRanges, gplots, graphics, grDevices, harmonicmeanp, heatmaply, htmltools, httr, IRanges, jsonlite, lattice, log4r, magrittr, MASS, Matrix, methods, NBPSeq, pander, parallel, qvalue, rmarkdown, rmdformats, Rsamtools, RSQLite, rtracklayer, S4Vectors, stats, stringr, SummarizedExperiment, survcomp, utils, VennDiagram, vsn, yaml, zoo
LinkingTo
Suggests BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit
SystemRequirements
Enhances TCC
URL http://www.fleming.gr
BugReports https://github.com/pmoulos/metaseqR2/issues
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
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/metaseqR2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metaseqR2
Package Short Url https://bioconductor.org/packages/metaseqR2/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: