Package: GenomicFeatures 1.65.0

H. Pagès

GenomicFeatures: Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Authors:H. Pagès [aut, cre], M. Carlson [aut], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], D. Sarkar [aut], M. Lawrence [aut], V. Obenchain [aut], S. Arora [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], P. Shannon [ctb], L. Shepherd [ctb], D. Tenenbaum [ctb], D. Van Twisk [ctb]

# Install 'GenomicFeatures' in R:

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

Bug tracker:https://github.com/bioconductor/genomicfeatures/issues

On BioConductor:GenomicFeatures-1.65.0(bioc 3.24)GenomicFeatures-1.64.0(bioc 3.23)

genetics infrastructure annotation sequencing genomeannotation bioconductor-package core-package

13.93 score 27 stars 359 packages 8.2k scripts 141 mentions 51 exports 66 dependencies

Last updated from:41960e538f. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	701
linux-devel-arm64	NOTE	995
linux-devel-x86_64	NOTE	1070
source / vignettes	OK	1078
linux-release-arm64	NOTE	940
linux-release-x86_64	NOTE	1035
macos-release-arm64	NOTE	702
macos-release-x86_64	NOTE	1182
macos-oldrel-arm64	NOTE	570
macos-oldrel-x86_64	NOTE	918
windows-devel	NOTE	856
windows-release	NOTE	809
windows-oldrel	NOTE	864
wasm-release	OK	712

Exports:as.list asBED asGFF cds cdsBy cdsByOverlaps coverageByTranscript distance exonicParts exons exonsBy exonsByOverlaps extendExonsIntoIntrons extractTranscriptSeqs extractUpstreamSeqs features fiveUTRsByTranscript genes getPromoterSeq getTerminatorSeq id2name intronicParts intronsByTranscript isActiveSeq isActiveSeq<-mapFromTranscripts mapIdsToRanges mapRangesToIds mapToTranscripts organism pcoverageByTranscript pmapFromTranscripts pmapToTranscripts promoters proteinToGenome seqinfo seqlevels<-seqlevels0 show terminators threeUTRsByTranscript tidyExons tidyIntrons tidyTranscripts transcriptLengths transcriptLocs2refLocs transcripts transcriptsBy transcriptsByOverlaps transcriptWidths tRNAs

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

Obtaining and Utilizing TxDb Objects

Rendered fromGenomicFeatures.Rmdusingknitr::rmarkdown

Last update: 2024-03-12
Started: 2022-01-21

Help page	Topics
Coerce to file format structures	asBED,TxDb-method asGFF,TxDb-method
Compute coverage by transcript (or CDS) of a set of ranges	coverageByTranscript pcoverageByTranscript
Extract non-overlapping exonic or intronic parts from a TxDb-like object	exonicParts intronicParts tidyExons tidyIntrons tidyTranscripts
Extend exons by a given number of bases into their adjacent introns	extendExonsIntoIntrons
Extract transcript (or CDS) sequences from chromosome sequences	extractTranscriptSeqs extractTranscriptSeqs,ANY-method extractTranscriptSeqs,DNAString-method
Extract sequences upstream of a set of genes or transcripts	extractUpstreamSeqs extractUpstreamSeqs,GenomicRanges-method extractUpstreamSeqs,GRangesList-method extractUpstreamSeqs,TxDb-method
FeatureDb objects	class:FeatureDb FeatureDb FeatureDb-class
Extract simple features from a FeatureDb object	features features,FeatureDb-method
Get gene promoter or terminator sequences	getPromoterSeq getPromoterSeq,GRanges-method getPromoterSeq,GRangesList-method getTerminatorSeq getTerminatorSeq,GRanges-method getTerminatorSeq,GRangesList-method
Map internal ids to external names for a given feature type	id2name
Map IDs to Genomic Ranges	mapIdsToRanges mapIdsToRanges,TxDb-method
Map Genomic Ranges to IDs	mapRangesToIds mapRangesToIds,TxDb-method
Map range coordinates between transcripts and genome space	coordinate-mapping coordinate-mapping-methods mapFromTranscripts mapFromTranscripts,GenomicRanges,GenomicRanges-method mapFromTranscripts,GenomicRanges,GRangesList-method mapToTranscripts mapToTranscripts,ANY,TxDb-method mapToTranscripts,GenomicRanges,GenomicRanges-method mapToTranscripts,GenomicRanges,GRangesList-method pmapFromTranscripts pmapFromTranscripts,GenomicRanges,GenomicRanges-method pmapFromTranscripts,GenomicRanges,GRangesList-method pmapFromTranscripts,IntegerRanges,GenomicRanges-method pmapFromTranscripts,IntegerRanges,GRangesList-method pmapToTranscripts pmapToTranscripts,GenomicRanges,GenomicRanges-method pmapToTranscripts,GenomicRanges,GRangesList-method pmapToTranscripts,GRangesList,GRangesList-method
Finding the nearest genomic range neighbor in a TxDb	distance,GenomicRanges,TxDb-method nearest-methods
Map protein-relative coordinates to genomic coordinates	proteinToGenome proteinToGenome,ANY-method proteinToGenome,GRangesList-method
Using the "select" interface on TxDb objects	columns,TxDb-method keys,TxDb-method keytypes,TxDb-method select,TxDb-method select-methods
Extract the transcript lengths (and other metrics) from a TxDb object	transcriptLengths
Converting transcript-based locations into reference-based locations	transcriptLocs2refLocs transcriptWidths
Extract genomic features from a TxDb-like object	cds cds,TxDb-method exons exons,TxDb-method genes genes,TxDb-method promoters promoters,TxDb-method terminators terminators,TxDb-method transcripts transcripts,TxDb-method
Extract and group genomic features of a given type from a TxDb-like object	cdsBy cdsBy,TxDb-method exonsBy exonsBy,TxDb-method fiveUTRsByTranscript fiveUTRsByTranscript,TxDb-method intronsByTranscript intronsByTranscript,TxDb-method threeUTRsByTranscript threeUTRsByTranscript,TxDb-method transcriptsBy transcriptsBy,TxDb-method
Extract genomic features from a TxDb-like object based on their genomic location	cdsByOverlaps cdsByOverlaps,TxDb-method exonsByOverlaps exonsByOverlaps,TxDb-method transcriptsByOverlaps transcriptsByOverlaps,TxDb-method
Extract tRNA genomic ranges from an object	tRNAs tRNAs,TxDb-method
TxDb objects	as.list,TxDb-method class:TxDb isActiveSeq isActiveSeq,TxDb-method isActiveSeq<- isActiveSeq<-,TxDb-method organism,TxDb-method saveRDS,TxDb-method seqinfo,TxDb-method seqlevels0,TxDb-method seqlevels<-,TxDb-method show,TxDb-method TxDb TxDb-class

Package: GenomicFeatures 1.65.0

GenomicFeatures: Query the gene models of a given organism/assembly

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