GenomicFiles

DOI: 10.18129/B9.bioc.GenomicFiles    

This is the development version of GenomicFiles; for the stable release version, see GenomicFiles.

Distributed computing by file or by range

Bioconductor version: Development (3.15)

This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

Author: Bioconductor Package Maintainer Obenchain <maintainer at bioconductor.org>, Valerie Love <maintainer at bioconductor.org>, Michael Shepherd <maintainer at bioconductor.org>, Lori Morgan <maintainer at bioconductor.org>, Martin Obenchain <maintainer at bioconductor.org>

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("GenomicFiles")):

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("GenomicFiles")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

PDF   Reference Manual
Video   Reading from a BAM file - Part 2

Details

biocViews Coverage, DataImport, Genetics, Infrastructure, Sequencing, Software
Version 1.31.0
In Bioconductor since BioC 2.14 (R-3.1) (7.5 years)
License Artistic-2.0
Depends R (>= 3.1.0), methods, BiocGenerics(>= 0.11.2), MatrixGenerics, GenomicRanges(>= 1.31.16), SummarizedExperiment, BiocParallel(>= 1.1.0), Rsamtools(>= 1.17.29), rtracklayer(>= 1.25.3)
Imports GenomicAlignments(>= 1.7.7), IRanges, S4Vectors(>= 0.9.25), VariantAnnotation(>= 1.27.9), GenomeInfoDb
LinkingTo
Suggests BiocStyle, RUnit, genefilter, deepSNV, snpStats, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
SystemRequirements
Enhances
URL
Depends On Me erma
Imports Me CAGEfightR, contiBAIT, derfinder, ldblock, QuasR, Rqc, VCFArray
Suggests Me TFutils
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/GenomicFiles
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicFiles
Package Short Url https://bioconductor.org/packages/GenomicFiles/
Package Downloads Report Download Stats

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