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customProDB (version 1.12.0)

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

Description

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

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Version

Version

1.12.0

License

Artistic-2.0

Maintainer

Xiaojing Wang

Last Published

February 15th, 2017

Functions in customProDB (1.12.0)

Outputaberrant

generate FASTA file containing short INDEL
OutputVarproseq_single

Output the variant(SNVs) protein sequences into FASTA format
PrepareAnnotationRefseq

prepare annotation for Refseq
easyRun

An integrated function to generate customized protein database for a single sample
Varlocation

Annotates the variations with genomic location.
InputVcf

Generate a list of GRanges objects from a VCF file.
Multiple_VCF

Generate shared variation dataset from multiple VCF files
SharedJunc

Generate shared junctions dataset from multiple BED files
Bed2Range

Generate a GRanges objects from BED file.
OutputVarproseq

Output the variant(SNVs) protein sequences into FASTA format
OutputsharedPro

Output the sequences of proteins with high expressions in multiple samples.
JunctionType

Annotates the junctions in a bed file.
Positionincoding

Find the position in coding sequence for each variation.
OutputNovelJun

generate peptide FASTA file that contains novel junctions.
calculateRPKM

Caculate RPKM for each transcripts based on exon read counts.
easyRun_mul

An integrated function to generate consensus protein database from multiple samples
PrepareAnnotationEnsembl

prepare annotation from ENSEMBL
Outputproseq

output FASTA format file contains proteins that have expression level above the cutoff
aaVariation

get the functional consequencece of SNVs located in coding region