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