IntEREst
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see IntEREst.
Intron-Exon Retention Estimator
Bioconductor version: 3.19
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("IntEREst")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles |
| Imports | seqLogo, Biostrings, GenomicFeatures, txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMySQL, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2 |
| System Requirements | |
| URL |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | IntEREst_1.28.0.tar.gz |
| Windows Binary (x86_64) | IntEREst_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | IntEREst_1.28.0.tgz |
| macOS Binary (arm64) | IntEREst_1.28.0.tgz |
| 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/ |
| Package Downloads Report | Download Stats |