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

Documentation for package ‘customProDB’ version 1.32.0

aaVariation	get the functional consequencece of SNVs located in coding region
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 database for a single sample
easyRun_mul	An integrated function to generate consensus protein database from multiple samples
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 expression level above the cutoff
OutputsharedPro	Output the sequences of proteins with high expressions in multiple samples.
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.