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

Generate customized protein sequence database from RNA-Seq data for proteomics search

Authorxiaojing wang
Date of publicationNone
Maintainerxiaojing wang <xiaojing.wang@bcm.edu>
LicenseArtistic-2.0
Version1.14.0

View on Bioconductor

Files in this package

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

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