vanallenlab/schadendorf-pd1

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vanallenlab/schadendorf-pd1

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

comut

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

retained-intron-neoantigen-pipeline

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

moalmanac

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

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

facets

Implementation of FACETS for Terra

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.

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

beanie

Tool for group biology estimation in single-cell RNAseq data

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.

phial

Precision Heuristics for Interpreting the Alteration Landscape

pnet

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

Jupyter Notebook

deconstruct_sigs_py

DeconstructSigs algorithm in python.

common_variant_filter

A simple filter to annotate and filter somatic or germline variants based on their observed allele counts in ExAC

2017-tcga-mc3_phial

Cohort analysis of TCGA mc3 with PHIAL

Jupyter Notebook

OncoPathwayDraw

Jupyter Notebook

microhet-paper

Jupyter Notebook

2016-Mouw_ASCC

Mouw et. al 2016, Genomic Evolution After Chemoradiotherapy in Anal Squamous Cell Carcinoma

Jupyter Notebook

mc_lightning_public

ped_germline_SV

Analysis of germline SVs in pediatric cancers

Jupyter Notebook

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.

automated_DbGaP_DataRetrieval

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

mpcproject-paper

A repository that contains code and data used to generate the figures for the MPCproject manuscript

Jupyter Notebook

VALab_Bi_He_ccRCC_scRNASeq_2021

r2d2

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

Jupyter Notebook

mapq_plotter

single_cell_help

Vignettes and scripts for pre-processing and analysis of single-cell and single-nuclei RNA-Seq data

Jupyter Notebook

training_with_abstention

Code supporting manuscript doi: https://doi.org/10.1101/2021.09.14.460365

Jupyter Notebook

SpliceJunctionVisualization

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

moalmanac-portal

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

moalmanac-browser

Web portal interface for browsing the Molecular Oncology Almanac

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.

2017-aacr_phial2

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

Jupyter Notebook

miniconda

Dockerfiles for Miniconda