eisaR

DOI: 10.18129/B9.bioc.eisaR    

This is the development version of eisaR; for the stable release version, see eisaR.

Exon-Intron Split Analysis (EISA) in R

Bioconductor version: Development (3.12)

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 "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.1.2
In Bioconductor since BioC 3.11 (R-4.0) (< 6 months)
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_1.1.2.tar.gz
Windows Binary eisaR_1.1.2.zip
macOS 10.13 (High Sierra) eisaR_1.1.2.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

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