alpine

DOI: 10.18129/B9.bioc.alpine  

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.17 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see alpineData.

alpine

Bioconductor version: 3.17

Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

Author: Michael Love, Rafael Irizarry

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("alpine")

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("alpine")

 

HTML	R Script	alpine
PDF		Reference Manual
Text		NEWS

Details

biocViews	AlternativeSplicing, BatchEffect, Coverage, DifferentialSplicing, GeneExpression, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Visualization
Version	1.26.0
In Bioconductor since	BioC 3.4 (R-3.3) (7 years)
License	GPL (>=2)
Depends	R (>= 3.5.0)
Imports	Biostrings, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm, splines, graph, RBGL, stringr, stats, methods, graphics, GenomeInfoDb, S4Vectors
LinkingTo
Suggests	knitr, testthat, markdown, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer
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	alpine_1.26.0.tar.gz
Windows Binary	alpine_1.26.0.zip
macOS Binary (x86_64)	alpine_1.26.0.tgz
macOS Binary (arm64)	alpine_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/alpine
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/alpine
Package Short Url	https://bioconductor.org/packages/alpine/
Package Downloads Report	Download Stats