Man pages for chambm/customProDB
Generate customized protein databases from NGS data for proteomics search

aaVariationget the functional consequencece of SNVs located in coding...
Bed2RangeGenerate a GRanges objects from BED file.
calculateRPKMCaculate RPKM for each transcripts based on exon read counts.
current_script_filecurrent script file (in full path)
customProDBCustomProDB
easyRunAn integrated function to generate customized protein...
easyRun_mulAn integrated function to generate consensus protein database...
expect_equal_to_referenceExpectation: is the object equal to a reference value stored...
fastComplementPure R function to turn a character vector of nucleotides...
getCodingFastaUrlFromUCSCGet URL to download coding sequence FASTA from UCSC genome...
getProteinFastaUrlFromUCSCGet URL to download protein sequence FASTA from UCSC genome...
getVariantAnnotationGet genome annotations for variants called in one or more VCF...
InputVcfGenerate a list of GRanges objects from a VCF file.
JunctionTypeAnnotates the junctions in a bed file.
Multiple_VCFGenerate shared variation dataset from multiple VCF files
Outputaberrantgenerate FASTA file containing short INDEL
OutputNovelJungenerate peptide FASTA file that contains novel junctions.
Outputproseqoutput FASTA format file contains proteins that have...
OutputsharedProOutput the sequences of proteins with high expressions in...
OutputVarprocodingseqOutput the variant(SNVs) protein coding sequences
OutputVarproseqOutput the variant(SNVs) protein sequences into FASTA format
OutputVarproseq_singleOutput the variant(SNVs) protein sequences into FASTA format
PositionincodingFind the position in coding sequence for each variation.
PrepareAnnotationEnsemblprepare annotation from ENSEMBL
PrepareAnnotationGCFPrepare an annotation set from an NCBI GCF assembly.
PrepareAnnotationRefseqprepare annotation for Refseq
read_or_update_local_cacheRead the cached result of an expression from a locally cached...
SharedJuncGenerate shared junctions dataset from multiple BED files
variantTypeGet the type of variant given one or more reference alleles...
VarlocationAnnotates the variations with genomic location.
chambm/customProDB documentation built on Feb. 22, 2019, 12:10 a.m.