Repositories list

• TRIBAL_PARSE_preprocess

  Public
  Python

  •0•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• MACH2

  Public
  Python

  •

  Other

  •0•2•0•0•Updated Dec 5, 2024Dec 5, 2024

• CloneTreeViz

  Public
  JavaScript

  •0•0•0•0•Updated Nov 29, 2024Nov 29, 2024

• Pharming

  Public
  Solves the clonal tree inference with copy numbers problem

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

• fastppm

  Public
  C++

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• TRIBAL_Dandelion_Preprocess

  Public
  JavaScript

  •0•0•0•0•Updated Nov 17, 2024Nov 17, 2024

• mach2-viz

  Public
  Cancer Metastasis and Clonal History (2) visualizer and exploratory tool

  JavaScript

  •

  MIT License

  •1•4•0•0•Updated Nov 4, 2024Nov 4, 2024

• derna

  Public
  RNA sequence design for a target protein sequence

  C

  •

  BSD 3-Clause "New" or "Revised" License

  •2•9•1•0•Updated Oct 30, 2024Oct 30, 2024

• CNRein

  Public
  Single-Cell Copy Number Calling with Evolution-Aware Deep Reinforcement Learning

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•1•0•Updated Oct 16, 2024Oct 16, 2024

• clonesim

  Public
  Simulating clonal trees with segmental CNAs and SNVs

  C++

  •0•2•0•0•Updated Oct 2, 2024Oct 2, 2024

• TRIBAL

  Public
  C

  •

  BSD 3-Clause "New" or "Revised" License

  •0•4•1•0•Updated Sep 11, 2024Sep 11, 2024

• Sapling

  Public
  Python

  •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

• cloneviz

  Public
  JavaScript

  •0•1•0•0•Updated Jun 4, 2024Jun 4, 2024

• phertilizer

  Public
  Phertilizer: growing a clonal tree from ultra-low coverage single-cell DNA sequencing data of tumors

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•4•1•0•Updated May 4, 2024May 4, 2024

• phyolin

  Public
  C++

  •1•2•2•0•Updated Feb 27, 2024Feb 27, 2024

• mach2-docs

  Public
  Documentation for MACH2

  0•0•0•0•Updated Jan 18, 2024Jan 18, 2024

• CloMu

  Public
  CloMu is a neural network based software for cancer phylogeny analysis.

  Python

  •

  MIT License

  •1•5•0•1•Updated Jan 13, 2024Jan 13, 2024

• PCCH

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Jan 8, 2024Jan 8, 2024

• CORSID-data

  Public
  HTML

  •0•0•0•0•Updated Nov 11, 2023Nov 11, 2023

• cnaviz

  Public
  Jupyter Notebook

  •5•12•3•0•Updated Nov 6, 2023Nov 6, 2023

• UniPPM

  Public
  Almost Uniform Sampling of Cancer Phylogenies from Bulk DNA Sequencing Data

  C++

  •0•0•0•0•Updated Jul 6, 2023Jul 6, 2023

• Jumper

  Public
  Discontinuous Transcript Assembly in Nidovirales

  Python

  •

  MIT License

  •1•0•1•0•Updated Jun 30, 2023Jun 30, 2023

• paction

  Public
  C++

  •0•1•0•0•Updated Jun 30, 2023Jun 30, 2023

• CORSID

  Public
  TRS and gene identifier

  pythonbioinformatics

  Python

  •

  MIT License

  •1•4•0•0•Updated May 9, 2023May 9, 2023

• SPhyR

  Public
  Single-cell Phylogeny Reconstruction

  Brainfuck

  •

  BSD 3-Clause "New" or "Revised" License

  •3•8•2•0•Updated Dec 9, 2022Dec 9, 2022

• phertilizer_data

  Public
  The accompanying data repository for Phertilizer

  0•2•0•0•Updated Oct 19, 2022Oct 19, 2022

• RECAP

  Public
  Detecting Evolutionary Patterns of Cancers using Consensus Trees

  Jupyter Notebook

  •2•3•1•0•Updated Oct 18, 2022Oct 18, 2022

• bcr-phylo-iso-benchmark

  Public
  updating simulation and pipeline to

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •8•0•0•0•Updated Oct 12, 2022Oct 12, 2022

• CORSID-viz

  Public
  Vue

  •0•0•2•0•Updated Aug 31, 2022Aug 31, 2022

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated May 24, 2022May 24, 2022