Package: ProteoDisco 1.19.0

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]

ProteoDisco_1.19.0.tar.gz
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ProteoDisco_1.19.0.tgz(r-4.6-any)ProteoDisco_1.19.0.tgz(r-4.5-any)
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ProteoDisco_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ProteoDisco/json (API)

# Install 'ProteoDisco' in R:

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

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

Datasets:

ProteoDiscographyExample.hg19 - Example ProteoDiscography.

On BioConductor:ProteoDisco-1.19.0(bioc 3.24)ProteoDisco-1.18.0(bioc 3.23)

software proteomics rnaseq snp sequencing variantannotation dataimport

5.48 score 5 stars 4 scripts 16 exports 91 dependencies

Last updated from:13dc81426f. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	330
linux-devel-x86_64	WARNING	763
source / vignettes	OK	621
linux-release-x86_64	WARNING	713
macos-release-arm64	WARNING	359
macos-oldrel-arm64	WARNING	345
windows-devel	WARNING	567
windows-release	WARNING	591
windows-oldrel	WARNING	634
wasm-release	OK	310

Exports:checkProteotypicFragments exportProteoDiscography generateJunctionModels generateProteoDiscography getDiscography importGenomicVariants importGenomicVariants.MAF importGenomicVariants.VCF importSpliceJunctions importTranscriptSequences incorporateGenomicVariants mutantTranscripts setGenomicSequences setMutantTranscripts setTxDb show

Dependencies:abind AnnotationDbi askpass backports BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem checkmate cigarillo cleaver cli codetools cpp11 crayon curl DBI DelayedArray dplyr fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise memuse mime openssl ParallelLogger pillar pkgconfig plyr png purrr R6 Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML xml2 XVector yaml

Overview of Proteodisco

Rendered fromOverview_ProteoDisco.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Checks if mutations and reference genome correspond	.checkReferenceAnchor
Determine proteotypic fragments within the translated CDS	checkProteotypicFragments 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 ProteoDiscography	importGenomicVariants
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 ProteoDiscography	importTranscriptSequences
Incorporate genomic events into their overlapping exonic sequences	incorporateGenomicVariants
Adds mutant transcript sequences to the ProteoDiscography in the appropriate slot	mutantTranscripts
ProteoDiscography	ProteoDiscography-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 slot	mutantTranscripts,ProteoDiscography-method setMutantTranscripts setMutantTranscripts,ProteoDiscography-method
Change the underlying TxDb of a ProteoDiscography object.	setTxDb setTxDb,ProteoDiscography-method