TBD

RNA sequencing experiments require intensive bioinformatics support. We present online tools designed to move raw sequencing data through various analysis packages with the goal of providing testable hypotheses.  Frnakenstein is a web based tool that accepts fastq files, maps the sequences to annotated genomes, determines gene expression levels, and can compare between biological states using four different analyses packages (CuffDiff, Bayseq,DeSeq2 and EdgeR).  PathBubbles can then visualize the results in the context of Reactome pathways, helping identify affected signaling and metabolic pathways.  WebGIVI can accept input expression data and visualize the genes in the context of eGIFT iTerms, placing gene names in biological contexts. WebGIVI also provides a means to rapidly connect from graphs to sentences extracted from the literature supporting the association between the gene and biological context. Finally, iGEP connects input gene lists to kinase substrate pairs found in the gene list. This can be used to generate biological hypotheses regarding metabolic or signaling events modulated by phosphorylation.