IntEREst

DOI: 10.18129/B9.bioc.IntEREst    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see IntEREst.

Intron-Exon Retention Estimator

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") 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	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL-2
Depends	R (>= 3.4), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors
Imports	seqLogo, Biostrings, GenomicFeatures, 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_1.8.0.tar.gz
Windows Binary	IntEREst_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	IntEREst_1.8.0.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