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alpine

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

alpine

Bioconductor version: Release (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")
alpine HTML R Script
Reference Manual PDF
NEWS Text

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
Linking To
Suggests knitr, testthat, markdown, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer
System Requirements
Enhances
URL
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Depends On Me
Imports Me
Suggests Me
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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
Old Source Packages for BioC 3.17 Source Archive