IntEREst

DOI: 10.18129/B9.bioc.IntEREst    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see IntEREst.

Intron-Exon Retention Estimator

Bioconductor version: 3.12

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 "4.0") and enter:

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

BiocManager::install("IntEREst")

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

Documentation

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

browseVignettes("IntEREst")

 

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

Details

biocViews Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 3.5 (R-3.4) (4 years)
License GPL-2
Depends R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors
Imports seqLogo, Biostrings, GenomicFeatures(>= 1.39.4), IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2
LinkingTo
Suggests clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package IntEREst_1.14.0.tar.gz
Windows Binary IntEREst_1.14.0.zip
macOS 10.13 (High Sierra) IntEREst_1.14.0.tgz
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/
Package Downloads Report Download Stats

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