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IntEREst

This is the development version of IntEREst; for the stable release version, see IntEREst.

Intron-Exon Retention Estimator

Bioconductor version: Development (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")):

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("IntEREst")

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

Documentation

Reference Manual PDF

Details

biocViews Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software
Version 1.25.1
In Bioconductor since BioC 3.5 (R-3.4) (6.5 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
Linking To
Suggests clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary IntEREst_1.25.1.zip
macOS Binary (x86_64) IntEREst_1.25.1.tgz
macOS Binary (arm64)
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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