Description from GitHub: "GenomicRanges-based classes for representing, querying, and manipulating matrices of genomic data (ie a map of pairs of genomic coordinates to a numeric value). Applications include visualization and analysis of Hi-C contact maps, barcode overlap in 10X, microhomology heatmaps, pairwise LD, and epistasis."

Description from GitHub: "This repository contains R scripts to reproduce the five figures in Chi et al., "High resolution analyses of associations between medications, microbiome and mortality in cancer patients". R folder contains the key script for PARADIGM algorithm. RMD folder contains the scripts to produce Figures 1-5 in the paper."

A jupyter notebook detailing the workflow, including data preprocessing, of running Palantir along with a demonstration of various plots and visualizations

Code for data analysis and visualization from "Epigenetic plasticity cooperates with cell-cell interactions to direct pancreatic tumorigenesis," (Burdziak et. al.). Includes a notebook with the full basic analysis of the PDAC progression data. See article for more information.

This dataset contains summary data visualizations and clinical data from target sequencing analysis of 2509 primary breast tumors from 2,509 patients. The study was conducted to identify putative cancer genes, revealing novel subgroups with distinct clinical outcomes. The results were validated by long-term clinical follow-up. The clinical data includes mutated genes, 3-gene classifier subtypes, and...

This dataset contains summary data visualizations and clinical data from targeted sequencing of 25040 tumors from 24950 patients and their matched normals via MSK-IMPACT, along with clinical annotations, some of which are derived from natural language processing (denoted NLP). This data is available under the Creative Commons BY-NC-ND 4.0 license. For commercial use, please contact datarequests@mskcc.org....