raphael-group Goto Github PK

absence-aware-clustering

ancestree

An algorithm for clonal tree reconstruction from multi-sample cancer sequencing data

arch

Algorithms for Reconstructing Cancer Histories

bca

belayer

bnpy

Bayesian nonparametric machine learning for Python

calder

CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data

calicost

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

carta

chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links

chisel-data

CHISEL-DATA -- This is a preliminary repository

cna-processing

Script for taking the output of the GISTIC2.0 module and converting the data for use with MAGI, HotNet2, and CoMEt.

cnd-aliquoting

cnt-ilp

Integer Linear Program for the Copy-Number Tree Problem

cnt-md

Software for inferring the copy-number profiles of tumor clones and their evolution from fractional copy numbers obtained from multi-sample bulk sequencing data.

comet

CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer

condor

copulacci

decifer

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

decifer-data

Input data and results

dest_ot

Developmental Spatiotemporal Optimal Transport

dialect

fastbe

gaston

gd3

Javascript library for visualizing genomics data with D3.

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

hatchet-paper

Related to (Zaccaria and Raphael, 2018), the repository contains the simulated data, the results of all methods involved in the comparison, the results of HATCHet on the prostate and pancreas cancer datasets, and all data and analysis related to these last two cancer datasets.

hatchet2-paper

Publication repository for results that accompany the HATCHet2 paper.

hatchet2-simulations

Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions

heinz

Single species module discovery