metaseqR2

DOI: 10.18129/B9.bioc.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 (3.12)

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>

Citation (from within R, enter citation("metaseqR2")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

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 1.1.23
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.1.23.tar.gz
Windows Binary metaseqR2_1.1.23.zip
macOS 10.13 (High Sierra) metaseqR2_1.1.23.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

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