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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 (3.19)

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 "4.4") 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
Reading from a BAM file - Part 2 Video

Details

biocViews Coverage, DataImport, Genetics, Infrastructure, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 2.14 (R-3.1) (10 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
System Requirements
URL
See More
Suggests BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
Linking To
Enhances
Depends On Me erma, IntEREst
Imports Me CAGEfightR, contiBAIT, derfinder, gDNAx, QuasR, Rqc, VCFArray
Suggests Me ldblock, MungeSumstats, TFutils
Links To Me
Build Report Build Report

Package Archives

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

Source Package GenomicFiles_1.39.0.tar.gz
Windows Binary GenomicFiles_1.39.0.zip
macOS Binary (x86_64) GenomicFiles_1.39.0.tgz
macOS Binary (arm64) GenomicFiles_1.39.0.tgz
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/
Package Downloads Report Download Stats