This repository contains scripts to identify healthy and malignant cells from scRNAseq with CloneTracer and process data from Optimized 10x libraries

Gene fusion detection and visualization

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).

Snakemake-based workflow for detecting structural variants in WGS data

dN/dS methods to quantify selection in cancer and somatic evolution

Utility functions for FACETS

Highly performant data storage in C++ for importing, querying and transforming variant data with C/C++/Java/Spark bindings. Used in gatk4.

Copy number calling and variant classification using targeted short read sequencing

Make Complex Heatmaps

Somatic copy variant caller (CNV) for next generation sequencing

An R package for predicting HR deficiency from mutation contexts

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.

LiFD is a two-phase algorithm to predict likely functional driver (LiFD) mutations that integrates information from multiple databases and bioinformatic methods.

CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either …

Bayesian mixture models for estimating and clustering cancer cell fractions

An R package for studying mutational and structural variant signatures along clonal evolution in cancer.

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

Create mutation signatures from MAF's, and decompose them into Stratton signatures

REVOLVER - Repeated Evolution in Cancer

Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.

Inferring selection in cancer sequencing data using ABC and population based simulations