jh2663's repositories
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.
LiFD
LiFD is a two-phase algorithm to predict likely functional driver (LiFD) mutations that integrates information from multiple databases and bioinformatic methods.
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