Beast code in Giters

raphael-group's repositories

hotnet2

HotNet2 is an algorithm for finding significantly altered subnetworks in a large gene interaction network

Language:PythonNOASSERTION98 19 19

Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.

Language:Python70 17 22

hierarchical-hotnet

Hierarchical HotNet is an algorithm for finding hierarchies of active subnetworks.

Language:PythonNOASSERTION36 11 4

machina

Framework for Metastatic And Clonal History INtegrative Analysis

Language:Jupyter NotebookBSD-3-Clause33 16 18

netNMF-sc

netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

Language:Jupyter NotebookBSD-3-Clause22 8 5

STARCH

Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity

Language:PythonMIT18 9 16

NAIBR

Novel Adjacency Identification with Barcoded Reads

Language:PythonMIT14 13 21

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.

Language:Python10 110

mascote

MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution) is a simulation framework to generate sequencing reads with appropriately corrections for the differences in genome lengths between the normal and tumor clone(s) present in multiple mixed samples.

Language:PythonNOASSERTION10 90