eisaR
This is thereleased version of eisaR; for the devel version, seeeisaR.
Exon-Intron Split Analysis (EISA) in R
Bioconductor version: Release (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("eisaR")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("eisaR")For older versions of R, please refer to the appropriateBioconductor 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 | 1.22.1 |
| In Bioconductor since | BioC 3.11 (R-4.0) (5.5 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,withr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | eisaR_1.22.1.tar.gz |
| Windows Binary (x86_64) | eisaR_1.22.1.zip (64-bit only) |
| macOS Binary (x86_64) | eisaR_1.22.1.tgz |
| macOS Binary (arm64) | eisaR_1.22.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/eisaR |
| 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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.22 | Source Archive |