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 (3.21)

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 "4.5") 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

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

Need some help? Ask on the Bioconductor Support site!

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	1.19.0
In Bioconductor since	BioC 3.11 (R-4.0) (4.5 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, txdbmaker, utils, VennDiagram, vsn, yaml, zoo
System Requirements
URL	http://www.fleming.gr
Bug Reports	https://github.com/pmoulos/metaseqR2/issues

Suggests	BiocStyle, BiocManager, BSgenome, knitr, RMySQL, RUnit
Linking To
Enhances	TCC
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	metaseqR2_1.19.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/metaseqR2/
Package Short Url	https://bioconductor.org/packages/metaseqR2/
Package Downloads Report	Download Stats