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metaseqR2

This is the development version of metaseqR2; for the stable release version, see metaseqR2.

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("metaseqR2")

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

Documentation

Reference Manual PDF

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 1.13.0
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
Linking To
Suggests BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit
System Requirements
Enhances TCC
URL http://www.fleming.gr
Bug Reports https://github.com/pmoulos/metaseqR2/issues
See More
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package
Windows Binary metaseqR2_1.13.0.zip
macOS Binary (x86_64) metaseqR2_1.13.0.tgz
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
Bioc Package Browser https://code.bioconductor.org/browse/metaseqR2/
Package Short Url https://bioconductor.org/packages/metaseqR2/
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