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eisaR

Exon-Intron Split Analysis (EISA) in R

Bioconductor version: 3.23 · Package version: 1.24.0

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.

Installation

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

BiocManager::install("eisaR")

Details

MaintainerMichael Stadler <michael.stadler@fmi.ch>
AuthorMichael Stadler [aut, cre], Dimos Gaidatzis [aut], Lukas Burger [aut], Charlotte Soneson [aut]
LicenseGPL-3
URLhttps://github.com/fmicompbio/eisaR
Bug Reportshttps://github.com/fmicompbio/eisaR/issues
Downloads rank393
Source branchRELEASE_3_23
biocViewsFunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics

Documentation

Download

Dependencies

Depends: R (>= 4.1)

Imports: graphics, stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils

Suggests: knitr, rmarkdown, testthat, BiocStyle, QuasR, Rbowtie, Rhisat2, Biostrings, BSgenome, BSgenome.Hsapiens.UCSC.hg38, ensembldb, AnnotationDbi, GenomicFeatures, txdbmaker, rtracklayer, withr