IntEREst

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

Intron-Exon Retention Estimator

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DOI: 10.18129/B9.bioc.IntEREst

Bioconductor version: Development (3.23)

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>

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

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software

Version 1.35.0

In Bioconductor since BioC 3.5 (R-3.4) (8.5 years)

License GPL-2

Depends R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles

Imports seqLogo, Biostrings, GenomicFeatures(>= 1.39.4), txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMariaDB, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2

System Requirements

URL

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 (x86_64)

macOS Binary (x86_64)

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

Package Short Url https://bioconductor.org/packages/IntEREst/

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