Pediatric Cancer Transcriptome Explorer (PCAT), http://www.pedtranscriptome.org
PCAT is a web portal that provides instance access to genomic and transcriptomic data of pediatric cancer. It integrates resources from several large scale consortium efforts, and importantly, provides preclinical testing data on more than 60 therapeutic agents from PPTC/PPTP.
Expression based Telomerase Enzymatic activity Detection (EXTEND)
Telomerase is active in stem cells and most cancer cells but not normal somatic cells. Telomerase activity is associated with cancer and many age related degenerative diseases. So far there is no reliable method to predict telomerase activity in large datasets. We developed EXTEND and extensively validated its performance in cell lines and other sources. We are wrapping it up for publication.
Tools I developed during training:
TCGA fusion portal, an online resource that catalogues all fusions identified from TCGA. Link is here.
PRADA, a pipeline for RNAseq processing and fusion calling. Written in python. Link is here. A recent update by us is available here on Github.
dmGWAS, a network based tool for Genome Wide Association Studies (GWAS). Written in R. Link is here.
GenRev, a network based tool for identifying gene interactions. Written in python. Link is here.