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GenomicFiles (development version)

GenomicFiles

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

Distributed computing by file or by range

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DOI: 10.18129/B9.bioc.GenomicFiles

Bioconductor version: Development (3.23)

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")):

Installation

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


if (!require("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

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataImport, Genetics, Infrastructure, Sequencing, Software

Version 1.47.0

In Bioconductor since BioC 2.14 (R-3.1) (11.5 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

See More

Suggests BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats

Linking To

Enhances

Depends On Me

Imports Me CAGEfightR, derfinder, gDNAx, QuasR, Rqc, TFutils, VCFArray

Suggests Me ldblock, MungeSumstats

Links To Me

Build Report Build Report

Package Archives

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

Source Package GenomicFiles_1.47.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/GenomicFiles

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicFiles

Bioc Package Browser https://code.bioconductor.org/browse/GenomicFiles/

Package Short Url https://bioconductor.org/packages/GenomicFiles/

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