Man pages for Bioconductor-mirror/customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

aaVariationget the functional consequencece of SNVs located in coding...
Bed2RangeGenerate a GRanges objects from BED file.
calculateRPKMCaculate RPKM for each transcripts based on exon read counts.
easyRunAn integrated function to generate customized protein...
easyRun_mulAn integrated function to generate consensus protein database...
InputVcfGenerate a list of GRanges objects from a VCF file.
JunctionTypeAnnotates the junctions in a bed file.
Multiple_VCFGenerate shared variation dataset from multiple VCF files
Outputaberrantgenerate FASTA file containing short INDEL
OutputNovelJungenerate peptide FASTA file that contains novel junctions.
Outputproseqoutput FASTA format file contains proteins that have...
OutputsharedProOutput the sequences of proteins with high expressions in...
OutputVarprocodingseqOutput the variant(SNVs) protein coding sequences
OutputVarproseqOutput the variant(SNVs) protein sequences into FASTA format
OutputVarproseq_singleOutput the variant(SNVs) protein sequences into FASTA format
PositionincodingFind the position in coding sequence for each variation.
PrepareAnnotationEnsemblprepare annotation from ENSEMBL
PrepareAnnotationRefseqprepare annotation for Refseq
SharedJuncGenerate shared junctions dataset from multiple BED files
VarlocationAnnotates the variations with genomic location.
Bioconductor-mirror/customProDB documentation built on June 1, 2017, 6:47 a.m.