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    61 repositories

    • pancan_germline_wgs

      Public
      Germline WGS variant calling across cancer types
      R
      •
      GNU General Public License v2.0
      •0•0•0•1•Updated Dec 13, 2024Dec 13, 2024

    • moalmanac

      Public
      Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine
      pythonmolecular-oncology-almanacprecision-cancer-medicineclinical-interpretation-algorithm
      HTML
      •
      GNU General Public License v2.0
      •5•16•0•1•Updated Dec 11, 2024Dec 11, 2024

    • germline-somatic-convergence

      Public
      Pilot exploration of overlap between germline and somatic alterations in common adult solid tumors
      R
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Dec 6, 2024Dec 6, 2024

    • moalmanac-db

      Public
      Underlying content for the Molecular Oncology Almanac's database
      precision-cancer-medicinemolecular-oncology-almanac
      GNU General Public License v2.0
      •1•5•0•0•Updated Dec 6, 2024Dec 6, 2024

    • beanie-analysis

      Public
      Code for reproducing results presented in the BEANIE paper
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Nov 15, 2024Nov 15, 2024

    • miniconda

      Public
      Dockerfiles for Miniconda
      Dockerfile
      •
      GNU General Public License v2.0
      •0•3•0•0•Updated Nov 5, 2024Nov 5, 2024

    • ped_germline_SV

      Public
      Analysis of germline SVs in pediatric cancers
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•2•0•0•Updated Oct 31, 2024Oct 31, 2024

    • comut

      Public
      CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
      Python
      •
      MIT License
      •28•90•10•4•Updated Aug 1, 2024Aug 1, 2024

    • schadendorf-pd1

      Public
      code and data for Liu, Schilling, et al Nat Med 2019
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •6•18•1•0•Updated Aug 1, 2024Aug 1, 2024

    • SigProfilerAssignment-wrapper

      Public
      Implementation repository for SigProfilerAssignment
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Jul 12, 2024Jul 12, 2024

    • EAC-multiome

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated May 30, 2024May 30, 2024

    • terra-helper

      Public
      Terra storage helper
      Python
      •
      GNU General Public License v2.0
      •0•0•4•2•Updated May 21, 2024May 21, 2024

    • moalmanac-browser

      Public
      Web portal interface for browsing the Molecular Oncology Almanac
      molecular-oncology-almanacpythonflask
      Python
      •
      GNU General Public License v2.0
      •1•1•1•2•Updated Apr 11, 2024Apr 11, 2024

    • moalmanac-paper

      Public archive
      Analyses related to Reardon et al. 2021, Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology
      paperprecision-cancer-medicinemolecular-oncology-almanac
      HTML
      •
      GNU General Public License v2.0
      •4•5•0•1•Updated Mar 13, 2024Mar 13, 2024

    • pnet

      Public
      Implementation of P-Net as a flexible deep learning tool to generate insights from genetic features.
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •5•7•1•0•Updated Feb 12, 2024Feb 12, 2024

    • microhet-paper

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•2•0•0•Updated Jan 17, 2024Jan 17, 2024

    • moalmanac-portal

      Public
      A cloud-based web portal for accessible clinical interpretation of integrative cancer genomics.
      pythonflaskmolecular-oncology-almanac
      HTML
      •
      GNU General Public License v2.0
      •3•1•3•5•Updated Oct 3, 2023Oct 3, 2023

    • .github

      Public
      About the Van Allen lab at Dana-Farber Cancer Institute
      GNU General Public License v2.0
      •0•0•0•0•Updated Sep 6, 2023Sep 6, 2023

    • beanie

      Public
      Tool for group biology estimation in single-cell RNAseq data
      bioinformaticsscrna-seqrobustnesssubsamplinggene-signaturessignature-scoringdifferential-enrichmentsingle-cell
      Python
      •
      GNU General Public License v2.0
      •1•5•0•0•Updated Aug 16, 2023Aug 16, 2023

    • 2023-cgc

      Public
      Repository with notebook and slides for 2023 Cancer Genome Consortium workshop on the Molecular Oncology Almanac (moalmanac.org)
      molecular-oncology-almanac
      HTML
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Aug 13, 2023Aug 13, 2023

    • 2017-aacr_phial2

      Public
      Computational analysis of clinically actionable genomic features: Precision Heuristics for Interpreting the Alteration Landscape (PHIAL) - AACR 2017
      cancervanallenlabbroadinstitutehhmidanafarberprecisionmedicine
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Feb 16, 2023Feb 16, 2023

    • 2017-tcga-mc3_phial

      Public
      Cohort analysis of TCGA mc3 with PHIAL
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •1•2•0•0•Updated Feb 16, 2023Feb 16, 2023

    • peds_ctDNA

      Public
      Algorithm for quantifying the number of translocation reads and wild-type reads in plasma samples with detectable ctDNA
      Shell
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 16, 2023Feb 16, 2023

    • abs_maf_clustering_vis

      Public
      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
      •
      GNU General Public License v2.0
      •2•1•0•0•Updated Feb 16, 2023Feb 16, 2023

    • maf_set_ops

      Public
      A class for calculating maf set intersections, with example scripts demonstrating usage.
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 16, 2023Feb 16, 2023

    • PyCloneTSVGeneration_FACETS_or_TITAN

      Public
      Combine snv maf, indel maf, and titan allelic copy number calls, from either FACETS or TITAN, into the .tsv input PyClone requires.
      Python
      •
      GNU General Public License v2.0
      •6•6•0•0•Updated Feb 16, 2023Feb 16, 2023

    • EnsemblToHGNC

      Public
      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
      •
      GNU General Public License v2.0
      •5•2•0•0•Updated Feb 16, 2023Feb 16, 2023

    • r2d2

      Public
      R2D2: RNA Normal/RNA Tumor, DNA Normal/DNA Tumor Analysis
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Feb 16, 2023Feb 16, 2023

    • armbander

      Public
      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
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Feb 16, 2023Feb 16, 2023

    • mapq_plotter

      Public
      Python
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Feb 16, 2023Feb 16, 2023