Package: customProDB 1.45.0

Xiaojing Wang

customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.

Authors:Xiaojing Wang

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NEWS

# Install 'customProDB' in R:

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

On BioConductor:customProDB-1.45.0(bioc 3.20)customProDB-1.44.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

20 exports 1.31 score 98 dependencies 7 mentions

Last updated 2 months agofrom:1030221703

Exports:aaVariation Bed2Range calculateRPKM easyRun easyRun_mul InputVcf JunctionType Multiple_VCF Outputaberrant OutputNovelJun Outputproseq OutputsharedPro OutputVarprocodingseq OutputVarproseq OutputVarproseq_single Positionincoding PrepareAnnotationEnsembl PrepareAnnotationRefseq SharedJunc Varlocation

Dependencies:abind AhoCorasickTrie AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr fansi fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue hms httr httr2 IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr plyr png prettyunits progress purrr R6 rappdirs Rcpp RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 VariantAnnotation vctrs withr XML xml2 XVector yaml zlibbioc

Introduction to customProDB

Rendered fromcustomProDB.Rnwusingutils::Sweaveon Jun 30 2024.

Last update: 2024-03-05
Started: 2013-11-01

Help page	Topics
get the functional consequencece of SNVs located in coding region	aaVariation
Generate a GRanges objects from BED file.	Bed2Range
Caculate RPKM for each transcripts based on exon read counts.	calculateRPKM
An integrated function to generate customized protein database for a single sample	easyRun
An integrated function to generate consensus protein database from multiple samples	easyRun_mul
Generate a list of GRanges objects from a VCF file.	InputVcf
Annotates the junctions in a bed file.	JunctionType
Generate shared variation dataset from multiple VCF files	Multiple_VCF
generate FASTA file containing short INDEL	Outputaberrant
generate peptide FASTA file that contains novel junctions.	OutputNovelJun
output FASTA format file contains proteins that have expression level above the cutoff	Outputproseq
Output the sequences of proteins with high expressions in multiple samples.	OutputsharedPro
Output the variant(SNVs) protein coding sequences	OutputVarprocodingseq
Output the variant(SNVs) protein sequences into FASTA format	OutputVarproseq
Output the variant(SNVs) protein sequences into FASTA format	OutputVarproseq_single
Find the position in coding sequence for each variation.	Positionincoding
prepare annotation from ENSEMBL	PrepareAnnotationEnsembl
prepare annotation for Refseq	PrepareAnnotationRefseq
Generate shared junctions dataset from multiple BED files	SharedJunc
Annotates the variations with genomic location.	Varlocation

Package: customProDB 1.45.0

customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Introduction to customProDB

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