Repositories list

• fmh_cosine_reproducibles

  Public
  Reproducibility code for the manuscript "Cosine similarity using FracMinHash sketches"

  Python

  •0•0•0•0•Updated Dec 31, 2024Dec 31, 2024

• sourmash_alternate_implementations

  Public
  Implement prefetch in cpp to investigate potential speedups

  Standard ML

  •3•0•9•0•Updated Dec 23, 2024Dec 23, 2024

• dnds-using-fmh

  Public
  Python

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

• YACHT

  Public
  A mathematically characterized hypothesis test for organism presence/absence in a metagenome

  C++

  •

  MIT License

  •8•30•10•3•Updated Dec 11, 2024Dec 11, 2024

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• fmh-funprofiler

  Public
  A functional profiler for metagenomes using FracMinHash

  Python

  •1•14•1•0•Updated Dec 4, 2024Dec 4, 2024

• DnDs-visualization

  Public
  A repo for the larger scale DnDs project, along with the visualization code

  Jupyter Notebook

  •

  MIT License

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

• afsampling

  Public
  Investigating cardinality of sketch sizes when sketching is done using affirmative sampling

  C++

  •1•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• KG2_SpanningTree_Analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

• prokrustean

  Public
  C++

  •

  GNU General Public License v3.0

  •0•3•1•0•Updated Nov 5, 2024Nov 5, 2024

• branch-lengths-assignment

  Public
  Python

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• frac-kmc

  Public
  Fast FracMinHash sketch generator

  C++

  •1•1•0•0•Updated Nov 3, 2024Nov 3, 2024

• fast_yacht_train

  Public
  This repository implements a faster version of yacht train

  C++

  •1•0•0•0•Updated Nov 2, 2024Nov 2, 2024

• DrugBankNER

  Public
  ETL of DrugBank to recognize KG2 concepts in DrugBank entries for use as training data

  Python

  •1•1•0•0•Updated Oct 29, 2024Oct 29, 2024

• Koslicki-lab-PSU

  Public
  Website for Koslicki Lab.

  bioinformaticscomputational-biologymetagenomics

  HTML

  •3•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• LLMFactCheck

  Public
  The "LLMFactCheck" is a powerful tool designed to semantic triples (subject–predicate–object) in different sources, ensuring the accuracy of references and enhancing the quality of your research.

  Python

  •

  MIT License

  •0•1•10•0•Updated Oct 13, 2024Oct 13, 2024

• Beta-diversity-of-mixtures-over-time

  Public
  Beta diversity of mixtures over time

  Python

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

• sourmash_tutorial

  Public
  0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

• KEGG_sketching_annotation_reproducibles

  Public
  Reproducible scripts for all KEGG + Sourmash gather computations for the associated paper

  Python

  •

  MIT License

  •1•0•0•0•Updated Jun 30, 2024Jun 30, 2024

• MetagenomicKG

  Public
  Python

  •4•13•1•0•Updated Jun 21, 2024Jun 21, 2024

• KG2_DrugMechDB_EA_Analysis

  Public
  Entity Alignment and Normalization between KG2 and DrugMechDB

  Jupyter Notebook

  •1•0•0•0•Updated May 5, 2024May 5, 2024

• FunUniFrac

  Public
  Functional UniFrac for metagenomic data

  Jupyter Notebook

  •

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

  •1•4•5•0•Updated Apr 12, 2024Apr 12, 2024

• YACHT_taxa_detector_experiments

  Public
  Python

  •0•2•0•0•Updated Mar 29, 2024Mar 29, 2024

• xDTD-analysis-Stephanie-rotation

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 14, 2024Feb 14, 2024

• FMH_vs_syncmer_reproducible

  Public
  Benchmark for k-mer setsof FMH vs open syncmer

  Python

  •0•1•0•0•Updated Jan 25, 2024Jan 25, 2024

• KEGG_sketching_annotation

  Public
  Scripts to sketch KEGG and explore using FracMinHash as a way to functionally annotate a metagenome

  Java

  •

  MIT License

  •2•2•7•1•Updated Nov 14, 2023Nov 14, 2023

• KGML-xDTD

  Public
  Forked version of Chunyu's xDTD model

  Python

  •

  MIT License

  •3•0•0•0•Updated Nov 8, 2023Nov 8, 2023

• YACHT-reproducibles

  Public
  A repo to reproduce the experiments in the YACHT manuscript

  Python

  •0•11•0•0•Updated Nov 2, 2023Nov 2, 2023

• .github

  Public
  Public profile

  0•0•0•0•Updated Sep 26, 2023Sep 26, 2023

• L2-UniFrac

  Public
  Expansion upon Median Unifrac to compute average phylogenetic distances between samples according to their UniFrac distance without producing negative abundance vectors.

  Python

  •0•1•9•0•Updated Aug 2, 2023Aug 2, 2023