Contacts
Sunghee Woo [suwoo at ucsd.edu], Seong Won Cha [s3cha at ucsd.edu], Stefano Bonissone [sbonisso at cs.ucsd.edu], Vineet Bafna [vbafna at cs.ucsd.edu]Summary
This tool-set is the downloadable list of all software development done during the Cancer Proteogenomics project [2013-2015] in CCMS.
The software is divided majorly into four components.
1. SpliceDB : Proteogenomic database for novel splice junction identifications driven from large-scale RNA-seq data. (input : BAM files, output : FASTA) [PMID: 23802565]
2. MutationDB : Proteogenomic database for identifying all types of mutatoinal variants driven from large-scale RNA-seq data. (input : VCF files, output : FASTA) [PMID: 25263569]
3. IG DB : Assembly based proteogenomic database for identifying complex immunoglobulin gene peptides. (input : BAM files, output : FASTA) [DOI: 10.1021/acs.jproteome.5b00264]
4. Post-processing tool (also called as Enosi) : Proteogenomic post-processing tools to assign proteogenomic events.
Documentation
Under preparation