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metaseqR2

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


Bioconductor version: Release (3.18)

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

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

browseVignettes("metaseqR2")
Building an annotation database for metaseqR2 HTML R Script
RNA-Seq data analysis with metaseqR2 HTML R Script
Reference Manual PDF
NEWS Text

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 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL (>= 3)
Depends R (>= 4.0.0), DESeq2, limma, locfit, splines
Imports ABSSeq, 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
System Requirements
URL http://www.fleming.gr
Bug Reports https://github.com/pmoulos/metaseqR2/issues
See More
Suggests BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit
Linking To
Enhances TCC
Depends On Me
Imports Me
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Links To Me
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Package Archives

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

Source Package metaseqR2_1.14.0.tar.gz
Windows Binary metaseqR2_1.14.0.zip
macOS Binary (x86_64) metaseqR2_1.14.0.tgz
macOS Binary (arm64) metaseqR2_1.14.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/metaseqR2
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/metaseqR2
Bioc Package Browser https://code.bioconductor.org/browse/metaseqR2/
Package Short Url https://bioconductor.org/packages/metaseqR2/
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