eisaR

DOI: 10.18129/B9.bioc.eisaR    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see eisaR.

Exon-Intron Split Analysis (EISA) in R

Bioconductor version: 3.11

Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

Author: Michael Stadler [aut, cre], Dimos Gaidatzis [aut], Lukas Burger [aut], Charlotte Soneson [aut]

Maintainer: Michael Stadler <michael.stadler at fmi.ch>

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("eisaR")

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("eisaR")

 

HTML	R Script	Generating reference files for spliced and unspliced abundance estimation with alignment-free methods
HTML	R Script	Using eisaR for Exon-Intron Split Analysis (EISA)
PDF		Reference Manual
Text		NEWS

Details

biocViews	FunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.11 (R-4.0) (0.5 years)
License	GPL-3
Depends	R (>= 4.0.0)
Imports	graphics, stats, GenomicRanges, GenomicFeatures, S4Vectors, IRanges, AnnotationDbi, limma, edgeR, methods, SummarizedExperiment, BiocGenerics, rtracklayer, utils
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb
SystemRequirements
Enhances
URL	https://github.com/fmicompbio/eisaR
BugReports	https://github.com/fmicompbio/eisaR/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	eisaR_1.0.0.tar.gz
Windows Binary	eisaR_1.0.0.zip
macOS 10.13 (High Sierra)	eisaR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/eisaR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/eisaR
Package Short Url	https://bioconductor.org/packages/eisaR/
Package Downloads Report	Download Stats