Repositories list

• fossilsim

  Public
  R package for simulating fossil data on phylogenetic trees under mechanistic models of preservation and sampling

  HTML

  •2•1•0•0•Updated Dec 13, 2024Dec 13, 2024

• TreeSim

  Public
  TreeSim — Simulating Phylogenetic Trees

  R

  •1•1•0•0•Updated Dec 12, 2024Dec 12, 2024

• lab

  Public
  Biological Data Science Lab website

  data-sciencegenomicsalgorithms+ 2biologymathematics

  HTML

  •0•0•1•0•Updated Dec 6, 2024Dec 6, 2024

• beast-phylonco

  Public
  A BEAST2 package for single-cell cancer evolution

  Java

  •

  GNU Lesser General Public License v2.1

  •2•7•16•0•Updated Dec 6, 2024Dec 6, 2024

• KAN-for-Binary-Phenotype-Classification

  Public
  TeX

  •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

• FBD-dLTTs

  Public
  Simulations for identifiability paper

  R

  •0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

• vcf2fasta

  Public
  Python

  •0•2•1•0•Updated Aug 13, 2024Aug 13, 2024

• VSTExprPhylo

  Public
  Scripts and analyses in Visium Spatial Transcriptomics phylogenetic analyses paper

  R

  •0•0•0•0•Updated Jun 12, 2024Jun 12, 2024

• tetres

  Public
  Package for discrete time trees

  Python

  •

  MIT License

  •0•3•1•0•Updated Apr 11, 2024Apr 11, 2024

• Pint

  Public
  Fast interactions lasso for sparse data

  C

  •

  MIT License

  •0•6•0•0•Updated Mar 26, 2024Mar 26, 2024

• castor

  Public
  Castor fork for sampled ancestor trees

  C++

  •1•0•0•0•Updated Jan 21, 2024Jan 21, 2024

• mixed_speciation_stratigraphic-ranges

  Public
  Java

  •5•0•0•0•Updated Dec 19, 2023Dec 19, 2023

• rrnni

  Public
  R package for RNNI distance

  cranrphylogenetics+ 2r-packager-stats

  C

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Aug 25, 2023Aug 25, 2023

• Centroid-Code

  Public
  This repository contains a Python implementation of the Centroid algorithm and a script to generate simulated datasets.

  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 15, 2023Aug 15, 2023

• rankedSPR

  Public
  Code for the ranked SPR paper, mostly experiments on diameters and shortest paths

  Python

  •

  MIT License

  •1•1•1•0•Updated May 16, 2023May 16, 2023

• treeOclock

  Public
  Implementation of algorithms in the RNNI space, e.g. FINDPATH

  C

  •

  MIT License

  •1•3•0•0•Updated Apr 3, 2023Apr 3, 2023

• seidel_compressed

  Public
  Seidel's Algorithm using Compressed Matrices (TurboPFor)

  C

  •0•0•0•0•Updated Jan 30, 2023Jan 30, 2023

• RNNI_code

  Public
  Python

  •0•1•1•0•Updated Jan 30, 2023Jan 30, 2023

• lasso_data_processing

  Public
  R

  •0•0•0•0•Updated Oct 23, 2022Oct 23, 2022

• snvformer

  Public
  Python

  •0•2•1•0•Updated Oct 14, 2022Oct 14, 2022

• dct_parser

  Public
  Python

  •0•0•0•0•Updated Sep 8, 2022Sep 8, 2022

• beast-phylonco-paper

  Public
  Data and analysis scripts to accompany BEAST phylonco

  Python

  •0•1•0•0•Updated Aug 21, 2022Aug 21, 2022

• phyloRNA

  Public
  A package to facilitate a phylogenetic analysis of scRNAseq data

  R

  •

  Other

  •1•7•0•0•Updated Jul 28, 2022Jul 28, 2022

• phyloRNAanalysis

  Public
  A phylogenetic analysis from scRNA-seq data using both expression levels and identified SNVs

  R

  •1•8•1•0•Updated Jun 8, 2022Jun 8, 2022

• beter

  Public
  R package to programatically create BEAST2 XMLs

  R

  •

  Other

  •0•2•1•0•Updated Jun 2, 2022Jun 2, 2022

• rnni_geometry_paper

  Public
  TeX

  •0•0•0•0•Updated Sep 11, 2021Sep 11, 2021

• xyz-simulation

  Public
  R

  •0•0•0•0•Updated Aug 7, 2021Aug 7, 2021

• rnni_polynomial_paper

  Public
  TeX

  •0•0•0•0•Updated Mar 11, 2021Mar 11, 2021

• RNNI_paper

  Public
  TeX

  •0•0•0•0•Updated Jul 3, 2020Jul 3, 2020