IntEREst

This is the released version of IntEREst; for the devel version, see IntEREst.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5

Intron-Exon Retention Estimator

Bioconductor version: Release (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")):

Ali Oghabian, Dario Greco, Mikko Frilander. IntEREst: Intron-Exon Retention Estimator. doi:10.18129/B9.bioc.IntEREst, R package version 1.36.0, https://bioconductor.org/packages/IntEREst.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software
Version	1.36.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	IntEREst_1.36.0.tar.gz
Windows Binary (x86_64)	IntEREst_1.36.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	IntEREst_1.36.0.tgz
macOS Binary (sonoma-arm64)	IntEREst_1.36.0.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