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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
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Depends On Me
Imports 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