alpine

DOI: 10.18129/B9.bioc.alpine    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see alpine.

alpine

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("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 1.8.0
In Bioconductor since BioC 3.4 (R-3.3) (2.5 years)
License GPL (>=2)
Depends R (>= 3.3)
Imports Biostrings, IRanges, GenomicRanges, GenomicAlignments, Rsamtools, SummarizedExperiment, GenomicFeatures, speedglm, splines, graph, RBGL, stringr, stats, methods, graphics, GenomeInfoDb, S4Vectors
LinkingTo
Suggests knitr, testthat, 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_1.8.0.tar.gz
Windows Binary alpine_1.8.0.zip
Mac OS X 10.11 (El Capitan) alpine_1.8.0.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 http://bioconductor.org/packages/alpine/
Package Downloads Report Download Stats

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