Package: txdbmaker 1.3.0

H. Pagès

txdbmaker: Tools for making TxDb objects from genomic annotations

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

Authors:H. Pagès [aut, cre], M. Carlson [aut], P. Aboyoun [aut], S. Falcon [aut], M. Morgan [aut], M. Lawrence [ctb], J. MacDonald [ctb], M. Ramos [ctb], S. Saini [ctb], L. Shepherd [ctb]

txdbmaker_1.3.0.tar.gz
txdbmaker_1.3.0.zip(r-4.5)txdbmaker_1.3.0.zip(r-4.4)txdbmaker_1.3.0.zip(r-4.3)
txdbmaker_1.3.0.tgz(r-4.4-any)txdbmaker_1.3.0.tgz(r-4.3-any)
txdbmaker_1.3.0.tar.gz(r-4.5-noble)txdbmaker_1.3.0.tar.gz(r-4.4-noble)
txdbmaker_1.3.0.tgz(r-4.4-emscripten)txdbmaker_1.3.0.tgz(r-4.3-emscripten)
txdbmaker.pdf |txdbmaker.html✨
txdbmaker/json (API)
NEWS

# Install 'txdbmaker' in R:
install.packages('txdbmaker', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

On BioConductor:txdbmaker-1.3.0(bioc 3.21)txdbmaker-1.2.0(bioc 3.20)

infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package

9.29 score 2 stars 87 packages 77 scripts 4.9k downloads 19 exports 92 dependencies

Last updated 23 days agofrom:942ba7269d. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxNOTEOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macNOTEOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macNOTEOct 31 2024

Exports:browseUCSCtrackgetChromInfoFromBiomartmakeFDbPackageFromUCSCmakeFeatureDbFromUCSCmakePackageNamemakeTxDbmakeTxDbFromBiomartmakeTxDbFromEnsemblmakeTxDbFromGFFmakeTxDbFromGRangesmakeTxDbFromUCSCmakeTxDbPackagemakeTxDbPackageFromBiomartmakeTxDbPackageFromUCSCsupportedMiRBaseBuildValuessupportedUCSCFeatureDbTablessupportedUCSCFeatureDbTrackssupportedUCSCtablesUCSCFeatureDbTableSchema

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydigestdplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryamlzlibbioc

Making TxDb Objects

Marc Carlson, Patrick Aboyoun, Hervé Pagès, Seth Falcon, Martin Morgan

Rendered fromtxdbmaker.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-04-04
Started: 2023-10-28

Readme and manuals

Help Manual

Help pageTopics
Tools for making TxDb objects from genomic annotationstxdbmaker-package txdbmaker
Making a FeatureDb object from annotations available at the UCSC Genome BrowsermakeFeatureDbFromUCSC supportedUCSCFeatureDbTables supportedUCSCFeatureDbTracks UCSCFeatureDbTableSchema
Making a TxDb object from user supplied annotationsmakeTxDb
Make a TxDb object from annotations available on a BioMart databasegetChromInfoFromBiomart makeTxDbFromBiomart
Make a TxDb object from an Ensembl databasemakeTxDbFromEnsembl
Make a TxDb object from annotations available as a GFF3 or GTF filemakeTxDbFromGFF
Make a TxDb object from a GRanges objectmakeTxDbFromGRanges
Make a TxDb object from annotations available at the UCSC Genome BrowserbrowseUCSCtrack makeTxDbFromUCSC supportedUCSCtables
Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source.makeFDbPackageFromUCSC makePackageName makeTxDbPackage makeTxDbPackageFromBiomart makeTxDbPackageFromUCSC supportedMiRBaseBuildValues