BiocFileCache

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

Manage Files Across Sessions

Bioconductor version: Development (3.24)

This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.

Author: Lori Shepherd [aut, cre], Martin Morgan [aut]

Maintainer: Lori Shepherd <lori.shepherd at roswellpark.org>

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

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("BiocFileCache")

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("BiocFileCache")

1. BiocFileCache Overview: Managing File Resources Across Sessions	HTML	R Script
2. BiocFileCache: Use Cases	HTML	R Script
3. BiocFileCache Troubleshooting	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, Software
Version	3.3.0
In Bioconductor since	BioC 3.5 (R-3.4) (9.5 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), dbplyr (>= 1.0.0)
Imports	methods, stats, utils, dplyr, RSQLite, DBI, filelock, curl, httr2
System Requirements
URL
Bug Reports	https://github.com/Bioconductor/BiocFileCache/issues

Suggests	testthat, knitr, BiocStyle, rmarkdown, rtracklayer
Linking To
Enhances
Depends On Me	AnnotationHub, easylift, ExperimentHub, RcwlPipelines, JASPAR2022, JASPAR2024, scATAC.Explorer, TMExplorer, csawBook, OSCA.advanced, OSCA.basic, OSCA.intro, OSCA.workflows
Imports Me	AlphaMissenseR, AMARETTO, atSNP, autonomics, BayesSpace, bedbaser, BiocBuildReporter, BiocCheck, BiocHail, BiocPkgTools, biomaRt, brendaDb, bugsigdbr, BulkSignalR, cbaf, cBioPortalData, CBNplot, CellBench, CTDquerier, customCMPdb, CytoPipeline, DeconvoBuddies, easyRNASeq, enhancerHomologSearch, EnMCB, EnrichmentBrowser, EpiTxDb, fenr, fgga, GeDi, GenomicScores, GenomicSuperSignature, ggkegg, GSEABenchmarkeR, gwascat, imageFeatureTCGA, iSEEindex, MBQN, MIRit, MotifPeeker, MsBackendMetaboLights, msPurity, OmicsMLRepoR, ontoProc, ORFik, OSTA.data, PhIPData, PlinkMatrix, PMScanR, postNet, psichomics, rBLAST, recount3, recountmethylation, regutools, ReUseData, RiboDiPA, rpx, scviR, sesame, signeR, SMTrackR, spacexr, SpatialExperiment, SpatialOmicsOverlay, SpliceImpactR, SpliceWiz, SurfR, tenXplore, terraTCGAdata, TFutils, tidyexposomics, tomoseqr, toppgene, tximeta, UMI4Cats, UniProt.ws, waddR, xenLite, geneplast.data, HPO.db, MPO.db, org.Mxanthus.db, PANTHER.db, BioPlex, bugphyzz, curatedBreastData, depmap, DNAZooData, fourDNData, HiContactsData, HumanRetinaLRSData, MetaScope, MicrobiomeBenchmarkData, NxtIRFdata, orthosData, SFEData, SingleCellMultiModal, spatialLIBD, OSTA, convertid
Suggests Me	anndataR, AnnotationForge, bambu, Bioc.gff, BiocSet, ChIPpeakAnno, CoGAPS, CRISPRseek, dominoSignal, EpiCompare, epiRomics, fastreeR, GRaNIE, HicAggR, HiCDCPlus, HiCExperiment, HiCool, ImageArray, iscream, MethReg, MetMashR, Nebulosa, nipalsMCIA, progeny, qsvaR, seqsetvis, spatialHeatmap, structToolbox, TCGAutils, TREG, visiumStitched, XeniumIO, zellkonverter, emtdata, EMTscoreData, HighlyReplicatedRNASeq, MethylSeqData, msigdb, TENxBrainData, TENxPBMCData, chipseqDB, fluentGenomics, simpleSingleCell, nemoR, scCustomize
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	BiocFileCache_3.3.0.tar.gz
Windows Binary (x86_64)	BiocFileCache_3.3.0.zip
macOS Binary (big-sur-x86_64)	BiocFileCache_3.3.0.tgz
macOS Binary (sonoma-arm64)	BiocFileCache_3.3.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocFileCache
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocFileCache
Bioc Package Browser	https://code.bioconductor.org/browse/BiocFileCache/
Package Short Url	https://bioconductor.org/packages/BiocFileCache/
Package Downloads Report	Download Stats