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

## Documentation for package ‘customProDB’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.