GenomicFiles

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14

Distributed computing by file or by range

Bioconductor version: Development (3.24)

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 [aut, cre], Valerie Obenchain [aut], Michael Love [aut], Lori Shepherd [aut], Martin Morgan [aut], Sonali Kumari [ctb] (Converted 'GenomicFiles' vignettes from Sweave to RMarkdown / HTML.)

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

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

Bioconductor Package Maintainer, Valerie Obenchain, Michael Love, Lori Shepherd, Martin Morgan. GenomicFiles: Distributed computing by file or by range. doi:10.18129/B9.bioc.GenomicFiles, R package version 1.49.0, https://bioconductor.org/packages/GenomicFiles.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("GenomicFiles")

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("GenomicFiles")

Introduction to GenomicFiles	HTML	R Script
Reference Manual	PDF
NEWS	Text
Video	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataImport, Genetics, Infrastructure, Sequencing, Software
Version	1.49.0
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	Artistic-2.0
Depends	BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools (>= 2.25.1), rtracklayer (>= 1.69.1), SummarizedExperiment (>= 1.39.1)
Imports	BiocBaseUtils, GenomeInfoDb (>= 1.45.7), GenomicAlignments (>= 1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation (>= 1.55.1)
System Requirements
URL	https://github.com/Bioconductor/GenomicFiles
Bug Reports	https://github.com/Bioconductor/GenomicFiles/issues

Suggests	BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats
Linking To
Enhances
Depends On Me	IntEREst
Imports Me	CAGEfightR, derfinder, gDNAx, QuasR, Rqc, TFutils, VCFArray
Suggests Me	ldblock, MungeSumstats, S4Cartographer
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	GenomicFiles_1.49.0.tar.gz
Windows Binary (x86_64)	GenomicFiles_1.49.0.zip
macOS Binary (big-sur-x86_64)	GenomicFiles_1.49.0.tgz
macOS Binary (sonoma-arm64)	GenomicFiles_1.49.0.tgz
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