Van Allen Lab's repositories
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
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.
2017-aacr_phial2
Computational analysis of clinically actionable genomic features: Precision Heuristics for Interpreting the Alteration Landscape (PHIAL) - AACR 2017
2017-tcga-mc3_phial
Cohort analysis of TCGA mc3 with PHIAL
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.
automated_DbGaP_DataRetrieval
FireCloud method that Retrieves DbGaP SRA files and converts them to BAM files
moalmanac-browser
Web portal interface for browsing the Molecular Oncology Almanac
moalmanac-portal
A cloud-based web portal for accessible clinical interpretation of integrative cancer genomics.
ped_germline_SV
Analysis of germline SVs in pediatric cancers
SpliceJunctionVisualization
FireCloud method: high-throughput visualization of splice junctions using ggsashimi package
germline-somatic-exploration-2023
Pilot exploration of overlap between germline and somatic alterations in common adult solid tumors
maf_set_ops
A class for calculating maf set intersections, with example scripts demonstrating usage.
pancan_germline_wgs
Germline WGS variant calling across cancer types
peds_ctDNA
Algorithm for quantifying the number of translocation reads and wild-type reads in plasma samples with detectable ctDNA
r2d2_allelic_imbalance
Allelic imbalance calculator
SigProfilerAssignment-wrapper
Implementation repository for SigProfilerAssignment
terra-helper
Terra storage helper