metaseqR2

DOI: 10.18129/B9.bioc.metaseqR2    

This package is for version 3.12 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: 3.12

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 [aut, cre]

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("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")

 

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

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	1.2.0
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
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	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	metaseqR2_1.2.0.tar.gz
Windows Binary	metaseqR2_1.2.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)	metaseqR2_1.2.0.tgz
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