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>

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