eisaR
Exon-Intron Split Analysis (EISA) in R
Bioconductor version: Release (3.19)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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 | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | eisaR_1.16.0.tar.gz |
| Windows Binary (x86_64) | eisaR_1.16.0.zip |
| macOS Binary (x86_64) | eisaR_1.16.0.tgz |
| macOS Binary (arm64) | eisaR_1.16.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/eisaR |
| Source Repository (Developer Access) | git clone [email protected]:packages/eisaR |
| Bioc Package Browser | https://code.bioconductor.org/browse/eisaR/ |
| Package Short Url | https://bioconductor.org/packages/eisaR/ |
| Package Downloads Report | Download Stats |