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

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

Author
xiaojing wang
Date of publication
None
Maintainer
xiaojing wang <xiaojing.wang@bcm.edu>
License
Artistic-2.0
Version
1.14.0

View on Bioconductor

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.

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