Package: ProteoDisco 1.13.0

Job van Riet

ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences

ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (variant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript sequences. The flexible workflow can be adopted to suit a myriad of research and experimental settings.

Authors:Job van Riet [cre], Wesley van de Geer [aut], Harmen van de Werken [ths]

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

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

Peer review:

Bug tracker:https://github.com/erasmusmc-ccbc/proteodisco/issues

Datasets:

On BioConductor:ProteoDisco-1.13.0(bioc 3.21)ProteoDisco-1.12.0(bioc 3.20)

softwareproteomicsrnaseqsnpsequencingvariantannotationdataimport

5.20 score 4 stars 4 scripts 142 downloads 16 exports 90 dependencies

Last updated 25 days agofrom:896da286e5. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winWARNINGNov 19 2024
R-4.5-linuxWARNINGNov 19 2024
R-4.4-winWARNINGNov 19 2024
R-4.4-macERRORNov 19 2024
R-4.3-winWARNINGNov 19 2024
R-4.3-macERRORNov 19 2024

Exports:checkProteotypicFragmentsexportProteoDiscographygenerateJunctionModelsgenerateProteoDiscographygetDiscographyimportGenomicVariantsimportGenomicVariants.MAFimportGenomicVariants.VCFimportSpliceJunctionsimportTranscriptSequencesincorporateGenomicVariantsmutantTranscriptssetGenomicSequencessetMutantTranscriptssetTxDbshow

Dependencies:abindAnnotationDbiaskpassbackportsBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcheckmatecleaverclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfansifastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslParallelLoggerpillarpkgconfigplogrplyrpngpurrrR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8VariantAnnotationvctrswithrXMLxml2XVectoryamlzlibbioc

Overview of Proteodisco

Job van Riet, Wesley van de Geer and Harmen van de Werken

Rendered fromOverview_ProteoDisco.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2021-11-17
Started: 2021-07-26

Readme and manuals

Help Manual

Help pageTopics
Checks if mutations and reference genome correspond.checkReferenceAnchor
Determine proteotypic fragments within the translated CDScheckProteotypicFragments checkProteotypicFragments,ProteoDiscography-method
Export the generated (mutant) peptides sequences to a FASTA database.exportProteoDiscography
Generate putative transcript-models derived from splice-junctions.generateJunctionModels
Generate the annotation database (ProteoDiscography)generateProteoDiscography
Retrieve imported genomic variants, splice-junctions and manual sequences.getDiscography getDiscography,ProteoDiscography-method
Import genomic variants into the ProteoDiscographyimportGenomicVariants
Import MAF files into a ProteoDiscography.importGenomicVariants.MAF
Import VCF files into a ProteoDiscography.importGenomicVariants.VCF
Import splice-junctions into the ProteoDiscograpy.importSpliceJunctions
Incorporate manual transcript sequences into the ProteoDiscographyimportTranscriptSequences
Incorporate genomic events into their overlapping exonic sequencesincorporateGenomicVariants
Adds mutant transcript sequences to the ProteoDiscography in the appropriate slotmutantTranscripts
ProteoDiscographyProteoDiscography-class
Example ProteoDiscography.ProteoDiscographyExample.hg19
Change the underlying genomic sequences of a ProteoDiscography object.setGenomicSequences setGenomicSequences,ProteoDiscography-method
Adds mutant transcript sequences to the ProteoDiscography in the appropriate slotmutantTranscripts,ProteoDiscography-method setMutantTranscripts setMutantTranscripts,ProteoDiscography-method
Change the underlying TxDb of a ProteoDiscography object.setTxDb setTxDb,ProteoDiscography-method