GenomicFiles

Distributed computing by file or by range

Bioconductor version: 3.23 · Package version: 1.48.0

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.

Installation

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

BiocManager::install("GenomicFiles")

Details

Maintainer	Bioconductor Package Maintainer <maintainer@bioconductor.org>
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.)
License	Artistic-2.0
URL	https://github.com/Bioconductor/GenomicFiles
Bug Reports	https://github.com/Bioconductor/GenomicFiles/issues
Downloads rank	1453
Source branch	RELEASE_3_23
biocViews	Coverage, DataImport, Genetics, Infrastructure, Sequencing, Software

Documentation

Introduction to GenomicFiles

Download

Follow the installation instructions to use this package in your R session.

Source package	GenomicFiles_1.48.0.tar.gz
Windows binary (x86_64)	GenomicFiles_1.48.0.zip
macOS binary (arm64)	GenomicFiles_1.48.0.tgz
macOS binary (x86_64)	GenomicFiles_1.48.0.tgz

Dependencies

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)

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

Reverse dependencies

Depends On Me (1): IntEREst

Imports Me (7): CAGEfightR, derfinder, gDNAx, QuasR, Rqc, TFutils, VCFArray

Suggests Me (2): ldblock, MungeSumstats