Introduction | Installing the txdbmaker package | Using makeTxDbFromUCSC | Using makeTxDbFromBiomart | Using makeTxDbFromEnsembl | Using makeTxDbFromGFF | Saving and Loading a TxDb Object | Using makeTxDbPackageFromUCSC and makeTxDbPackageFromBiomart | Session Information
Package: txdbmaker 1.9.0
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:
txdbmaker_1.9.0.tar.gz
txdbmaker_1.9.0.zip(r-4.7)txdbmaker_1.9.0.zip(r-4.6)txdbmaker_1.9.0.zip(r-4.5)
txdbmaker_1.9.0.tgz(r-4.6-any)txdbmaker_1.9.0.tgz(r-4.5-any)
txdbmaker_1.9.0.tar.gz(r-4.7-any)txdbmaker_1.9.0.tar.gz(r-4.6-any)
txdbmaker_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
txdbmaker/json (API)
| # Install 'txdbmaker' in R: |
| install.packages('txdbmaker', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/txdbmaker/issues
On BioConductor:txdbmaker-1.9.0(bioc 3.24)txdbmaker-1.8.0(bioc 3.23)
infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package
Last updated from:d57df0dab4. Checks:1 WARNING, 7 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 217 | ||
| linux-devel-x86_64 | ERROR | 636 | ||
| source / vignettes | OK | 321 | ||
| linux-release-x86_64 | ERROR | 567 | ||
| macos-release-arm64 | ERROR | 252 | ||
| macos-oldrel-arm64 | ERROR | 309 | ||
| windows-devel | ERROR | 503 | ||
| windows-release | ERROR | 500 | ||
| windows-oldrel | ERROR | 381 | ||
| wasm-release | OK | 150 |
Exports:browseUCSCtrackgetChromInfoFromBiomartmakeFDbPackageFromUCSCmakeFeatureDbFromUCSCmakePackageNamemakeTxDbmakeTxDbFromBiomartmakeTxDbFromEnsemblmakeTxDbFromGFFmakeTxDbFromGRangesmakeTxDbFromUCSCmakeTxDbPackagemakeTxDbPackageFromBiomartmakeTxDbPackageFromUCSCsupportedUCSCFeatureDbTablessupportedUCSCFeatureDbTrackssupportedUCSCtablesUCSCFeatureDbTableSchema
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Tools for making TxDb objects from genomic annotations | txdbmaker-package txdbmaker |
| Making a FeatureDb object from annotations available at the UCSC Genome Browser | makeFeatureDbFromUCSC supportedUCSCFeatureDbTables supportedUCSCFeatureDbTracks UCSCFeatureDbTableSchema |
| Making a TxDb object from user supplied annotations | makeTxDb |
| Make a TxDb object from annotations available on a BioMart database | getChromInfoFromBiomart makeTxDbFromBiomart |
| Make a TxDb object from an Ensembl database | makeTxDbFromEnsembl |
| Make a TxDb object from annotations available as a GFF3 or GTF file | makeTxDbFromGFF |
| Make a TxDb object from a GRanges object | makeTxDbFromGRanges |
| Make a TxDb object from annotations available at the UCSC Genome Browser | browseUCSCtrack makeTxDbFromUCSC supportedUCSCtables |
| Making a TxDb package from annotations available at the UCSC Genome Browser, biomaRt or from another source. | makeFDbPackageFromUCSC makePackageName makeTxDbPackage makeTxDbPackageFromBiomart makeTxDbPackageFromUCSC |
