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eisaR

Exon-Intron Split Analysis (EISA) in R


Bioconductor version: Release (3.18)

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 1.14.1
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-3
Depends R (>= 4.1)
Imports graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR(>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils
System Requirements
URL https://github.com/fmicompbio/eisaR
Bug Reports https://github.com/fmicompbio/eisaR/issues
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer
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Package Archives

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

Source Package eisaR_1.14.1.tar.gz
Windows Binary eisaR_1.14.1.zip
macOS Binary (x86_64) eisaR_1.14.1.tgz
macOS Binary (arm64) eisaR_1.14.1.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
Old Source Packages for BioC 3.18 Source Archive