vanallenlab/moalmanac-paper

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vanallenlab/moalmanac-paper

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

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.

schadendorf-pd1

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

Jupyter Notebook

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

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