Package: GenomicFiles 1.43.0

Bioconductor Package Maintainer

GenomicFiles: Distributed computing by file or by range

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.

Authors:Bioconductor Package Maintainer [aut, cre], Valerie Obenchain [aut], Michael Love [aut], Lori Shepherd [aut], Martin Morgan [aut], Sonali Kumari [ctb]

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GenomicFiles.pdf |GenomicFiles.html✨
GenomicFiles/json (API)
NEWS

# Install 'GenomicFiles' in R:

install.packages('GenomicFiles', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:GenomicFiles-1.41.0(bioc 3.20)GenomicFiles-1.40.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

genetics infrastructure dataimport sequencing coverage

6.75 score 15 packages 71 scripts 1.8k downloads 37 exports 70 dependencies

Last updated 20 days agofrom:dce61b1a10. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	WARNING	Oct 30 2024
R-4.5-linux	WARNING	Oct 30 2024
R-4.4-win	WARNING	Oct 30 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	WARNING	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:.fileTypeRegistry assay colData colData<-colnames countBam coverage files files<-findTypeRegistry GenomicFiles getVCFPath makeFileType pack paths1kg RangedVcfStack readVcfStack reduceByFile reduceByRange reduceByYield reduceFiles reduceRanges REDUCEsampler registerFileType rownames rowRanges rowRanges<-scanBam seqinfo seqinfo<-show summarizeOverlaps summary unpack vcfFields VcfStack yieldSize

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml zlibbioc

Introduction to GenomicFiles

Valerie Obenchain, Michael Love, Martin Morgan, Sonali Kumari

Rendered fromGenomicFiles.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-03-17
Started: 2023-03-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
GenomicFiles objects	class:GenomicFiles colData<-,GenomicFiles,DataFrame-method dimnames<-,GenomicFiles,list-method files files,GenomicFiles-method files<- files<-,GenomicFiles,character-method files<-,GenomicFiles,List-method GenomicFiles GenomicFiles,GenomicRanges_OR_GRangesList,character-method GenomicFiles,GenomicRanges_OR_GRangesList,List-method GenomicFiles,GenomicRanges_OR_GRangesList,list-method GenomicFiles,missing,ANY-method GenomicFiles,missing,missing-method GenomicFiles-class show,GenomicFiles-method [,GenomicFiles,ANY,ANY,ANY-method [,GenomicFiles,ANY,ANY-method
Deprecated functions in package 'GenomicFiles'	GenomicFiles-deprecated getVCFPath
Range transformations of a 'GenomicRanges' object for optimal file queries.	isPacked pack pack,GRanges-method
Parallel computations by files	reduceByFile reduceByFile,GenomicFiles,missing-method reduceByFile,GRanges,ANY-method reduceByFile,GRangesList,ANY-method reduceFiles
Parallel computations by ranges	reduceByRange reduceByRange,GenomicFiles,missing-method reduceByRange,GRanges,ANY-method reduceByRange,GRangesList,ANY-method reduceRanges
Iterate through a BAM (or other) file, reducing output to a single result.	reduceByYield REDUCEsampler
Functions for creating and searching a registry of file types.	findTypeRegistry makeFileType registerFileType registry-utils
Un-pack results obtained with a pack()ed group of ranges	unpack unpack,List,GRangesList-method unpack,list,GRangesList-method
VcfStack and RangedVcfStack Objects	assay,RangedVcfStack,ANY-method assay,VcfStack,ANY-method class:VcfStack colData,VcfStack-method colData<-,VcfStack,DataFrame-method colnames,VcfStack-method dim,VcfStack-method dimnames,VcfStack-method files,VcfStack-method files<-,VcfStack,character-method files<-,VcfStack,VcfFile-method files<-,VcfStack,VcfFileList-method paths1kg RangedVcfStack RangedVcfStack-class readVcfStack rownames,VcfStack-method rowRanges,RangedVcfStack-method rowRanges<-,RangedVcfStack,GRanges-method seqinfo,VcfStack-method seqinfo<-,RangedVcfStack-method seqinfo<-,VcfStack-method seqlevelsStyle<-,RangedVcfStack-method seqlevelsStyle<-,VcfStack-method show,VcfStack-method vcfFields,VcfStack-method VcfStack VcfStack-class [,RangedVcfStack,ANY,ANY,ANY-method [,RangedVcfStack,ANY,ANY-method [,VcfStack,ANY,ANY,ANY-method [,VcfStack,ANY,ANY-method