eisaR

Exon-Intron Split Analysis (EISA) in R

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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")

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

Details

biocViews	FunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics
Version	1.12.0
In Bioconductor since	BioC 3.11 (R-4.0) (3.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR, methods, SummarizedExperiment, BiocGenerics, utils
Linking To
Suggests	knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer
System Requirements
Enhances
URL	https://github.com/fmicompbio/eisaR
Bug Reports	https://github.com/fmicompbio/eisaR/issues

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	eisaR_1.12.0.tar.gz
Windows Binary	eisaR_1.12.0.zip (64-bit only)
macOS Binary (x86_64)	eisaR_1.12.0.tgz
macOS Binary (arm64)	eisaR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/eisaR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/eisaR
Bioc Package Browser	https://code.bioconductor.org/browse/eisaR/
Package Short Url	https://bioconductor.org/packages/eisaR/
Package Downloads Report	Download Stats