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Bioconductor - eisaR (development version)

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 (3.22)

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 "4.5") and enter:


if (!require("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")
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 1.21.0 In Bioconductor since BioC 3.11 (R-4.0) (5 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, txdbmaker, rtracklayer Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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