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MAAPER: Analysis of Alternative Polyadenylation Using 3' End-Linked Reads

A computational method developed for model-based analysis of alternative polyadenylation (APA) using 3' end-linked reads. It accurately assigns 3' RNA-seq reads to polyA sites through statistical modeling, and generates multiple statistics for APA analysis. Please also see Li WV, Zheng D, Wang R, Tian B (2021) <doi:10.1186/s13059-021-02429-5>.

Version: 1.1.1
Imports: parallel, GenomicRanges, GenomicAlignments, GenomicFeatures, GenomeInfoDb, stats, utils, Rsamtools, IRanges, MASS
Suggests: knitr, rmarkdown
Published: 2021-08-14
DOI: 10.32614/CRAN.package.MAAPER
Author: Wei Vivian Li ORCID iD [aut, cre]
Maintainer: Wei Vivian Li <vivian.li at rutgers.edu>
License: GPL-3
URL: https://github.com/Vivianstats/MAAPER, https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02429-5
NeedsCompilation: no
In views: Omics
CRAN checks: MAAPER results

Documentation:

Reference manual: MAAPER.pdf
Vignettes: MAAPER: Model-based analysis of alternative polyadenylation using 3' end-linked reads

Downloads:

Package source: MAAPER_1.1.1.tar.gz
Windows binaries: r-devel: MAAPER_1.1.1.zip, r-release: MAAPER_1.1.1.zip, r-oldrel: MAAPER_1.1.1.zip
macOS binaries: r-release (arm64): MAAPER_1.1.1.tgz, r-oldrel (arm64): MAAPER_1.1.1.tgz, r-release (x86_64): MAAPER_1.1.1.tgz, r-oldrel (x86_64): MAAPER_1.1.1.tgz
Old sources: MAAPER archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.