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
| Maintainer | Michael Stadler <michael.stadler@fmi.ch> |
| Author | Michael Stadler [aut, cre], Dimos Gaidatzis [aut], Lukas Burger [aut], Charlotte Soneson [aut] |
| License | GPL-3 |
| URL | https://github.com/fmicompbio/eisaR |
| Bug Reports | https://github.com/fmicompbio/eisaR/issues |
| Downloads rank | 393 |
| Source branch | RELEASE_3_23 |
| biocViews | FunctionalGenomics, GeneExpression, GeneRegulation, RNASeq, Regression, Software, Transcription, Transcriptomics |
Documentation
- Generating reference files for spliced and unspliced abundance estimation with alignment-free methods
- Using eisaR for Exon-Intron Split Analysis (EISA)
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