Van Allen Lab

comut

CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

facets

Implementation of FACETS for Terra

moalmanac

Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine

moalmanac-db

Underlying content for the Molecular Oncology Almanac's database

moalmanac-paper

Analyses related to Reardon et al. 2021, Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology

MutPanningV2

This repository contains the source code of the revised version of MutPanning. MutPanning is publicly available under the BSD3-Clause open source license.

neoantigen_calling_pipeline

Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA

PyCloneTSVGeneration_FACETS_or_TITAN

Combine snv maf, indel maf, and titan allelic copy number calls, from either FACETS or TITAN, into the .tsv input PyClone requires.

retained-intron-neoantigen-pipeline

Pipeline to call neoantigens from intron retention events derived from RNA-Seq data.

schadendorf-pd1

code and data for Liu, Schilling, et al Nat Med 2019

vanallenlab/comut

CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots

vanallenlab/moalmanac

Molecular Oncology Almanac, a clinical interpretation algorithm paired with a novel underlying knowledge base for precision cancer medicine

vanallenlab/PyCloneTSVGeneration_FACETS_or_TITAN

Combine snv maf, indel maf, and titan allelic copy number calls, from either FACETS or TITAN, into the .tsv input PyClone requires.

vanallenlab/moalmanac-db

Underlying content for the Molecular Oncology Almanac's database

vanallenlab/moalmanac-paper

Analyses related to Reardon et al. 2021, Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology

vanallenlab/beanie

Tool for group biology estimation in single-cell RNAseq data

vanallenlab/EnsemblToHGNC

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.

vanallenlab/ped_germline_SV

Analysis of germline SVs in pediatric cancers

vanallenlab/2017-aacr_phial2

Computational analysis of clinically actionable genomic features: Precision Heuristics for Interpreting the Alteration Landscape (PHIAL) - AACR 2017

vanallenlab/2017-tcga-mc3_phial

Cohort analysis of TCGA mc3 with PHIAL

vanallenlab/abs_maf_clustering_vis

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.

vanallenlab/automated_DbGaP_DataRetrieval

FireCloud method that Retrieves DbGaP SRA files and converts them to BAM files

vanallenlab/mapq_plotter

vanallenlab/microhet-paper

vanallenlab/miniconda

Dockerfiles for Miniconda

vanallenlab/moalmanac-browser

Web portal interface for browsing the Molecular Oncology Almanac

vanallenlab/moalmanac-portal

A cloud-based web portal for accessible clinical interpretation of integrative cancer genomics.

vanallenlab/pnet

Implementation of P-Net as a flexible deep learning tool to generate insights from genetic features.

vanallenlab/r2d2

R2D2: RNA Normal/RNA Tumor, DNA Normal/DNA Tumor Analysis

vanallenlab/SpliceJunctionVisualization

FireCloud method: high-throughput visualization of splice junctions using ggsashimi package

vanallenlab/.github

About the Van Allen lab at Dana-Farber Cancer Institute

vanallenlab/2023-cgc

Repository with notebook and slides for 2023 Cancer Genome Consortium workshop on the Molecular Oncology Almanac (moalmanac.org)

vanallenlab/armbander

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.

vanallenlab/germline-somatic-exploration-2023

Pilot exploration of overlap between germline and somatic alterations in common adult solid tumors

vanallenlab/maf_set_ops

A class for calculating maf set intersections, with example scripts demonstrating usage.

vanallenlab/pancan_germline_wgs

Germline WGS variant calling across cancer types

vanallenlab/peds_ctDNA

Algorithm for quantifying the number of translocation reads and wild-type reads in plasma samples with detectable ctDNA

vanallenlab/r2d2_allelic_imbalance

Allelic imbalance calculator

vanallenlab/SigProfilerAssignment-wrapper

Implementation repository for SigProfilerAssignment

vanallenlab/terra-helper

Terra storage helper