Van Allen Lab's repositories
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
neoantigen_calling_pipeline
Pipeline to call somatic cancer neoantigens from mutations in patient tumor DNA
MutPanningV2
This repository contains the source code of the revised version of MutPanning. MutPanning is publicly available under the BSD3-Clause open source license.
VanAllen_CTLA4_Science_RNASeq_TPM
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.
common_variant_filter
A simple filter to annotate and filter somatic or germline variants based on their observed allele counts in ExAC
deconstruct_sigs_py
DeconstructSigs algorithm in python.
2016-Mouw_ASCC
Mouw et. al 2016, Genomic Evolution After Chemoradiotherapy in Anal Squamous Cell Carcinoma
mpcproject-paper
A repository that contains code and data used to generate the figures for the MPCproject manuscript
training_with_abstention
Code supporting manuscript doi: https://doi.org/10.1101/2021.09.14.460365
call_cna_from_absolute
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
CLAM
Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
mcr
Dockers for Matlab Compiler Runtime (MCR)
moalmanac-cohort
Cohort analysis of samples analyzed by MOAlmanac
moalmanac-extension
Chrome extension for adding assertions to Molecular Oncology Almanac
moalmanac-matchmaking
Template repository to perform profile-to-cell line matchmaking
MSIsensor
Dockerized and FireCloud implementation for MSI sensor
process_coverage_info
Process outputs from GATK DepthOfCoverage tool
SpliceJunctionDiscovery
A multithreaded Python implementation of Beryl Cummings' MendelianRNA-seq algorithm
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
vt
Dockerfile for VT