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welcome to fiveprime welcome to fiveprime nathan siemers i am a consultant for research in pharmaceutical translational medicine with a heavy emphasis on genomics and bioinformatics i m cross trained in immunology oncology bioinformatics genomics and chemistry my training and experience have made able to integrate information and synthesize hypotheses and conclusions across diverse domains of science and medicine below is a small collection of tools i ve created to answer questions about cancer and immunology genomic studies including the analysis of single cell rna information t2 a new browser for the 2018 release of tcga pan cancer study group this tool captures and plots rna gene level mutation events mut position specific mutations fmut continuous and thresholded copy number estimates cnv and cnc signature projections subtype classifications purity estimates and much more it also contains advanced captilities for adjusting for biases and covariates in multi model tcga data faux flow viewer for single cell melanoma rna seq data there s only so much you can get out of a t sne or umap clustering i built tools that are modeled on the behavior of flow cytometry tools here s one that interrogates the tirosh et al melanoma paper fantastic paper faux flow viewer for single cell liver cancer rna seq data hepatocellular carcinoma t cell data set from zheng et al faux flow viewer for single cell blood derived monocytes and dendritic cells alexandra chloé villani et al results browser to support the 2017 siemers et al genome wide association study of tumor genetics with immune cell estimates link to paper unified tcga cancer target childhood cancer and gtex normal human tissue rna data browser many thanks to the ucsc xena team and the toil project to make unified data available network relationships of genes across tcga the plos paper referenced above used signatures for immune cell types that were derived from a mutual rank distance network across tcga in particular we discovered the association of ccr8 with tumor tregs using these networks the allnets application will let you interrogate these relationships across all of tcga or any specific tumor type