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 (3.18)

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")):


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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


biocViews FunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.1)
Imports graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR, methods, SummarizedExperiment, BiocGenerics, utils
Suggests knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, rtracklayer
URL https://github.com/fmicompbio/eisaR
BugReports https://github.com/fmicompbio/eisaR/issues
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Source Package eisaR_1.13.0.tar.gz
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macOS Binary (x86_64) eisaR_1.13.0.tgz
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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/
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