Man pages for chambm/customProDB
Generate customized protein databases from NGS 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. |
| current_script_file | current script file (in full path) |
| customProDB | CustomProDB |
| easyRun | An integrated function to generate customized protein... |
| easyRun_mul | An integrated function to generate consensus protein database... |
| expect_equal_to_reference | Expectation: is the object equal to a reference value stored... |
| fastComplement | Pure R function to turn a character vector of nucleotides... |
| getCodingFastaUrlFromUCSC | Get URL to download coding sequence FASTA from UCSC genome... |
| getProteinFastaUrlFromUCSC | Get URL to download protein sequence FASTA from UCSC genome... |
| getVariantAnnotation | Get genome annotations for variants called in one or more VCF... |
| 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 |
| PrepareAnnotationGCF | Prepare an annotation set from an NCBI GCF assembly. |
| PrepareAnnotationRefseq | prepare annotation for Refseq |
| read_or_update_local_cache | Read the cached result of an expression from a locally cached... |
| SharedJunc | Generate shared junctions dataset from multiple BED files |
| variantType | Get the type of variant given one or more reference alleles... |
| Varlocation | Annotates the variations with genomic location. |
