Repositories list

• derna

  Public
  RNA sequence design for a target protein sequence

  C

  •

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

  •3•13•2•0•Updated Oct 2, 2025Oct 2, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.6k•0•0•0•Updated Aug 29, 2025Aug 29, 2025

• MACH2

  Public
  Jupyter Notebook

  •

  Other

  •0•3•0•0•Updated Aug 29, 2025Aug 29, 2025

• CNRein

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

  Python

  •

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

  •2•1•2•0•Updated Aug 13, 2025Aug 13, 2025

• CloMu

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

  Python

  •

  MIT License

  •2•6•0•1•Updated Jul 29, 2025Jul 29, 2025

• fastppm

  Public
  C++

  •

  MIT License

  •0•1•0•0•Updated Jul 29, 2025Jul 29, 2025

• Sapling-data

  Public
  Sapling data

  Jupyter Notebook

  •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

• Sapling

  Public
  Python

  •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

• clonesim

  Public
  Simulating clonal trees with segmental CNAs and SNVs

  C++

  •0•2•0•0•Updated Jun 12, 2025Jun 12, 2025

• mach2-viz

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

  JavaScript

  •

  MIT License

  •1•5•0•0•Updated Jun 1, 2025Jun 1, 2025

• Dolphyin

  Public
  A phylogenetic inference method for 1-Dollo phylogenies

  Jupyter Notebook

  •0•1•0•0•Updated May 21, 2025May 21, 2025

• Pharming

  Public
  Solves the clonal tree inference with copy numbers problem

  Python

  •

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

  •0•2•0•0•Updated Feb 25, 2025Feb 25, 2025

• TRIBAL_PARSE_preprocess

  Public
  Python

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

• CloneTreeViz

  Public
  JavaScript

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

• TRIBAL_Dandelion_Preprocess

  Public
  JavaScript

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

• fastppm-data

  Public
  Python

  •0•0•0•0•Updated Oct 13, 2024Oct 13, 2024

• TRIBAL

  Public
  C

  •

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

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

• 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