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 (3.18)

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 "4.3") 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	1.37.0
In Bioconductor since	BioC 2.14 (R-3.1) (9.5 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
Linking To
Suggests	BiocStyle, RUnit, genefilter, deepSNV, snpStats, knitr, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens
System Requirements
Enhances
URL

Depends On Me	erma, IntEREst
Imports Me	CAGEfightR, contiBAIT, derfinder, QuasR, Rqc, VCFArray
Suggests Me	ldblock, MungeSumstats, TFutils
Links To Me
Build Report

Package Archives

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

Source Package	GenomicFiles_1.37.0.tar.gz
Windows Binary	GenomicFiles_1.37.0.zip
macOS Binary (x86_64)	GenomicFiles_1.37.0.tgz
macOS Binary (arm64)	GenomicFiles_1.37.0.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