Van Allen Lab

Clinical Computational Oncology @ Dana-Farber Cancer Institute and the Broad Institute of MIT & Harvard

  • FireCloud implementation of FACETS

    Jupyter Notebook Updated Oct 19, 2018
  • Dockerized and FireCloud implementation for MSI sensor

    wdl Updated Oct 10, 2018
  • Precision Heuristics for Interpreting the Alteration Landscape

    R 3 3 Updated Oct 6, 2018
  • DeconstructSigs algorithm in python.

    Python 1 Updated Oct 2, 2018
  • A simple filter to annotate and filter somatic variants based on their observed allele counts in ExAC

    Python MIT Updated Sep 19, 2018
  • FireCloud method: high-throughput visualization of splice junctions using ggsashimi package

    Python Updated Sep 17, 2018
  • A multithreaded Python implementation of Beryl Cummings' MendelianRNA-seq algorithm

    Python Updated Sep 12, 2018
  • A script that adds columns with arm and band-level information to any tab-separated file. Intended primarily for use with .seg-format files, but applicable across formats.

    Python Updated Aug 24, 2018
  • Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.

    Python 6 4 Apache-2.0 Updated Jul 30, 2018
  • R2D2: RNA Normal/RNA Tumor, DNA Normal/DNA Tumor Analysis

    Jupyter Notebook 1 Updated Jul 19, 2018
  • Format mutations for oncoprint

    Updated Jul 5, 2018
  • This script takes in a tab-separated file containing at least one column of Ensembl IDs and a string indicating the header for this column, and outputs a tab-separated file identical to the input file except that it has an additional column containing mapped HGNC gene symbols for each row.

    Python 1 Updated May 24, 2018
  • Combine snv maf, indel maf, and titan allelic copy number calls, from either FACETS or TITAN, into the .tsv input PyClone requires.

    Python 1 1 Updated May 23, 2018
  • Contains TPM matrix (produced by RSEM) for pre-treatment samples from N = 42 ipilimumab-treated melanoma patients published in Van Allen et al. Science 2015.

    1 Updated Apr 13, 2018
  • Dockerfiles for Miniconda

    Updated Apr 9, 2018
  • Mouw et. al 2016, Genomic Evolution After Chemoradiotherapy in Anal Squamous Cell Carcinoma

    Jupyter Notebook 1 Updated Apr 3, 2018
  • A class for calculating maf set intersections, with example scripts demonstrating usage.

    Python Updated Mar 14, 2018
  • Coding exercises for budding computational biologists

    R 1 Updated Feb 23, 2018
  • Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA

    Python 2 2 Updated Jan 18, 2018
  • Dockers for Matlab Compiler Runtime (MCR)

    Updated Dec 28, 2017
  • Given gene annotated segtab files from ABSOLUTE generate arm and band level annotations and calls for amplifications, LOH, and deletions based on process from Brastianos, Carter et al Cancer Discovery 2015

    Python Updated Dec 7, 2017
  • This workflow can be used to visualize the data from an *ABS_MAF.txt absolute file output. Both detection power and genomic locus are plotted for all SNPs, along with clustering information based on cancer cell fraction.

    Python Updated Nov 8, 2017
  • Algorithm for quantifying the number of translocation reads and wild-type reads in plasma samples with detectable ctDNA

    Shell Updated Nov 6, 2017
  • Cohort analysis of TCGA mc3 with PHIAL

    Jupyter Notebook 1 Updated Aug 22, 2017
  • Computational analysis of clinically actionable genomic features: Precision Heuristics for Interpreting the Alteration Landscape (PHIAL) - AACR 2017

    Jupyter Notebook 1 Updated Apr 20, 2017
  • Most used topics




    This organization has no public members. You must be a member to see who’s a part of this organization.