alpine

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see alpineData.

alpine

DOI: 10.18129/B9.bioc.alpine

Bioconductor version: 3.14

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 "4.1") 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")

alpine HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews AlternativeSplicing, BatchEffect, Coverage, DifferentialSplicing, GeneExpression, Normalization, QualityControl, RNASeq, Sequencing, Software, Transcription, Visualization

Version 1.20.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 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

System Requirements

URL

Suggests knitr, testthat, markdown, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer

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 alpine_1.20.0.tar.gz

Windows Binary alpine_1.20.0.zip

macOS 10.13 (High Sierra) alpine_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/alpine

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/alpine

Bioc Package Browser https://code.bioconductor.org/browse/alpine/

Package Short Url https://bioconductor.org/packages/alpine/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive