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 (3.24)
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("eisaR")):Michael Stadler, Dimos Gaidatzis, Lukas Burger, Charlotte Soneson. eisaR: Exon-Intron Split Analysis (EISA) in R. doi:10.18129/B9.bioc.eisaR, R package version 1.25.3, https://bioconductor.org/packages/eisaR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| Using eisaR for Exon-Intron Split Analysis (EISA) | HTML | R Script |
| Generating reference files for spliced and unspliced abundance estimation with alignment-free methods | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics |
| Version | 1.25.3 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | stats, GenomicRanges, S4Vectors, IRanges, limma, edgeR (>= 4.0), methods, SummarizedExperiment, BiocGenerics, utils, ggplot2, rlang |
| 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, withr |
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| Enhances | |
| Depends On Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | eisaR_1.25.3.tar.gz |
| Windows Binary (x86_64) | eisaR_1.25.3.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | eisaR_1.25.3.tgz |
| macOS Binary (sonoma-arm64) | eisaR_1.25.3.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 |