alpine
This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see alpineData.
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 (!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 | ||
| NEWS | Text |
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) (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 |
See More
| Suggests | knitr, testthat, 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_1.8.0.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 |
| 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 3.8 | Source Archive |