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brass

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

ccube

Bayesian mixture models for estimating and clustering cancer cell fractions

chord

An R package for predicting HR deficiency from mutation contexts

clonetracer

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

cnapp

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 aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model

cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing

complexheatmap

Make Complex Heatmaps

decifer

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

dndscv

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

facets

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

facets-suite

Utility functions for FACETS

genefuse

Gene fusion detection and visualization

genomicsdb

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

hrdetect-pipeline

lifd

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

mosdepth

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

mutation-signatures

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

palimpsest

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

pineapple-src

yuzu Early Access source code with linux specific patches included

purecn

Copy number calling and variant classification using targeted short read sequencing

revolver

REVOLVER - Repeated Evolution in Cancer

subclonalselection.jl

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

sv-callers

Snakemake-based workflow for detecting structural variants in WGS data

yuzu-mainline