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>

Citation (from within R, enter citation("alpine")):

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: