metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2  

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

Bioconductor version: Release (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>

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 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
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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