customProDB: Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Version 1.16.0

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.

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Authorxiaojing wang
Bioconductor views AlternativeSplicing MassSpectrometry Proteomics RNASeq SNP Software Transcription
Date of publicationNone
Maintainerxiaojing wang <xiaojing.wang@bcm.edu>
LicenseArtistic-2.0
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("customProDB")

Man pages

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

Functions

Bed2Range Man page Source code
Ensembl.fetchAttribTypeIdForTopLevelSequence Source code
Ensembl.fetchChromLengthsFromCoreUrl Source code
Ensembl.fetchTopLevelSequenceIds Source code
Ensembl.getFtpUrlToMySQL Source code
Ensembl.getMySQLCoreDir Source code
Ensembl.getMySQLCoreUrl Source code
Ensembl.getTable Source code
Ensembl.getTable.seq_region Source code
Ensembl.listMySQLCoreDirs Source code
InputVcf Man page Source code
JunctionType Man page Source code
Multiple_VCF Man page Source code
OutputNovelJun Man page Source code
OutputVarprocodingseq Man page Source code
OutputVarproseq Man page Source code
OutputVarproseq_single Man page Source code
Outputaberrant Man page Source code
Outputproseq Man page Source code
OutputsharedPro Man page Source code
Positionincoding Man page Source code
PrepareAnnotationEnsembl Man page Source code
PrepareAnnotationRefseq Man page Source code
SharedJunc Man page Source code
Varlocation Man page Source code
aaVariation Man page Source code
calculateRPKM Man page Source code
dbEasyPreparedQuery Source code
dbEasyQuery Source code
dbFileConnect Source code
debugSQL Source code
easyRun Man page Source code
easyRun_mul Man page Source code
extractCdsRangesFromBiomartTable Source code
extractEnsemblReleaseFromDbVersion Source code
extractSpeciesFromDatasetDesc Source code
fetchChromLengthsFromEnsembl Source code
gen_splicmatrix Source code Source code
getAllDatasetAttrGroups Source code
getBiomartDbVersion Source code
getChromInfoFromBiomart Source code
getDatasetAttrGroups Source code
getMartAttribList Source code
get_cached_dbconn Source code
get_cached_dbfile Source code
get_dbconn Source code
get_dbfile Source code
get_dbtable Source code
hasCol Source code
joinDataFrameWithName2Val Source code
lsFtpUrl Source code
makeBiomartChrominfo Source code
makeBiomartGenes Source code
makeBiomartSplicings Source code
makeBiomartTranscripts Source code
makeCdsDataFrameFromRanges Source code
makeExonRankCol Source code
makeIdsForUniqueDataFrameRows Source code
makeTranscriptDbFromBiomart_archive Source code
map2trans Source code
matchCircularity Source code
normUtrCoords Source code
parseBMFiltersParams Source code
parseBMMartParams Source code
parseBMValuesParams Source code
prepareBiomartMetadata Source code
scanMart Source code
scanMarts Source code
setDataFrameColClass Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/Bed2Range.R
R/Ensembl.utils.R
R/InputVcf.R
R/JunctionType.R
R/Multiple_VCF.R
R/OutputNovelJun.R
R/OutputVarprocodingseq.R
R/OutputVarproseq.R
R/OutputVarproseq_single.R
R/Outputaberrant.R
R/Outputproseq.R
R/OutputsharedPro.R
R/Positionincoding.R
R/PrepareAnnotationEnsembl.R
R/PrepareAnnotationRefseq.R
R/SharedJunc.R
R/Varlocation.R
R/aaVariation.R
R/calculateRPKM.R
R/easyRun.R
R/easyRun_mul.R
R/makeTranscriptDbFromBiomart_archive.R
R/utils.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/customProDB.R
inst/doc/customProDB.Rnw
inst/doc/customProDB.pdf
inst/extdata
inst/extdata/bams
inst/extdata/bams/test1_sort.bam
inst/extdata/bams/test1_sort.bam.bai
inst/extdata/bams/test2_sort.bam
inst/extdata/bams/test2_sort.bam.bai
inst/extdata/bams/test3_sort.bam
inst/extdata/bams/test3_sort.bam.bai
inst/extdata/beds
inst/extdata/beds/junctions1.bed
inst/extdata/beds/junctions2.bed
inst/extdata/beds/junctions3.bed
inst/extdata/refseq
inst/extdata/refseq/cosmic.RData
inst/extdata/refseq/dbsnpinCoding.RData
inst/extdata/refseq/exon_anno.RData
inst/extdata/refseq/ids.RData
inst/extdata/refseq/procodingseq.RData
inst/extdata/refseq/proseq.RData
inst/extdata/refseq/splicemax.RData
inst/extdata/refseq/txdb.sqlite
inst/extdata/refseq_coding_seq.fasta
inst/extdata/refseq_pro_seq.fasta
inst/extdata/test_mul.vcf
inst/extdata/tmp
inst/extdata/tmp/test_indel.fasta
inst/extdata/tmp/test_junc.fasta
inst/extdata/tmp/test_rpkm.fasta
inst/extdata/tmp/test_snv.fasta
inst/extdata/tmp/test_snv.tab
inst/extdata/vcfs
inst/extdata/vcfs/test1.vcf
inst/extdata/vcfs/test2.vcf
inst/extdata/vcfs/test3.vcf
man
man/Bed2Range.Rd
man/InputVcf.Rd
man/JunctionType.Rd
man/Multiple_VCF.Rd
man/OutputNovelJun.Rd
man/OutputVarprocodingseq.Rd
man/OutputVarproseq.Rd
man/OutputVarproseq_single.Rd
man/Outputaberrant.Rd
man/Outputproseq.Rd
man/OutputsharedPro.Rd
man/Positionincoding.Rd
man/PrepareAnnotationEnsembl.Rd
man/PrepareAnnotationRefseq.Rd
man/SharedJunc.Rd
man/Varlocation.Rd
man/aaVariation.Rd
man/calculateRPKM.Rd
man/easyRun.Rd
man/easyRun_mul.Rd
vignettes
vignettes/customProDB.Rnw
customProDB documentation built on May 20, 2017, 9:57 p.m.