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Intron-Exon Retention Estimator

Bioconductor version: Release (3.18)

This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

Author: Ali Oghabian <Ali.Oghabian at Helsinki.Fi>, Dario Greco <dario.greco at helsinki.fi>, Mikko Frilander <Mikko.Frilander at helsinki.fi>

Maintainer: Ali Oghabian <Ali.Oghabian at Helsinki.Fi>, Mikko Frilander <Mikko.Frilander at helsinki.fi>

Citation (from within R, enter citation("IntEREst")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

IntEREst, Intron Exon Retention Estimator HTML R Script
Reference Manual PDF


biocViews Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-2
Depends R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles
Imports seqLogo, Biostrings, GenomicFeatures(>= 1.39.4), IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2
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Suggests clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
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Follow Installation instructions to use this package in your R session.

Source Package IntEREst_1.26.0.tar.gz
Windows Binary IntEREst_1.26.0.zip
macOS Binary (x86_64) IntEREst_1.26.0.tgz
macOS Binary (arm64) IntEREst_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/IntEREst
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/IntEREst
Bioc Package Browser https://code.bioconductor.org/browse/IntEREst/
Package Short Url https://bioconductor.org/packages/IntEREst/
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