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. |