Repositories list

• METABOLIC

  Public
  A scalable high-throughput metabolic and biogeochemical functional trait profiler

  Perl

  •46•190•112•1•Updated Jan 27, 2025Jan 27, 2025

• protein_set_transformer

  Public
  Protein Set Transformer (PST) framework for training protein-language-model-based genome language models. Inference is possible for viral genomes using our pretrained viral foundation model.

  Jupyter Notebook

  •

  MIT License

  •3•5•1•0•Updated Jan 24, 2025Jan 24, 2025

• UKPeatlandViruses

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 6, 2025Jan 6, 2025

• ViWrap

  Public
  A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

  Python

  •15•70•31•1•Updated Dec 27, 2024Dec 27, 2024

• V-Score-Search

  Public
  Searchable Database for V-Scores from VOG, PHROG, KEGG, eggNOG, and Pfam

  JavaScript

  •1•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• vClassifier

  Public
  Species-level taxonomic classification of viruses

  Shell

  •

  GNU General Public License v3.0

  •0•3•2•0•Updated Dec 15, 2024Dec 15, 2024

• Clostridium_scindens_mining

  Public
  Shell

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• Prophage-DB

  Public
  Prophage-DB scripts for generating figures

  Jupyter Notebook

  •1•3•0•0•Updated Nov 15, 2024Nov 15, 2024

• ViromeVsMetagenome

  Public
  2•2•1•0•Updated Oct 7, 2024Oct 7, 2024

• Klier_et_al._2024_HMMs

  Public
  HMM's used in Klier et al. 2024 Manuscript on Evolution of Sulfur Metabolism

  0•0•0•0•Updated Aug 8, 2024Aug 8, 2024

• SulfurReviewPaper

  Public
  The procedures for Sulfur Review Paper

  Perl

  •0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

• .github

  Public
  0•0•0•0•Updated May 31, 2024May 31, 2024

• PropagAtE

  Public
  Prophage Activity Estimator

  Python

  •

  GNU General Public License v3.0

  •3•26•13•0•Updated May 30, 2024May 30, 2024

• TYMEFLIES_Viral

  Public
  The scripts for the project of "TYMEFLIES_Viral"

  Python

  •

  Other

  •1•2•0•0•Updated Apr 25, 2024Apr 25, 2024

• VIBRANT

  Public
  Virus Identification By iteRative ANnoTation

  Python

  •

  GNU General Public License v3.0

  •37•159•52•1•Updated Apr 15, 2024Apr 15, 2024

• Phage_T7

  Public
  0•0•0•0•Updated Jan 24, 2024Jan 24, 2024

• Diao_et_al_2023

  Public
  0•0•0•0•Updated Sep 11, 2023Sep 11, 2023

• annoVIBRANT

  Public
  Annotation-only wrapper for VIBRANT

  Python

  •0•3•0•0•Updated Jan 18, 2023Jan 18, 2023

• vRhyme

  Public
  Binning Virus Genomes from Metagenomes

  Python

  •

  GNU General Public License v3.0

  •10•61•28•0•Updated Jul 13, 2022Jul 13, 2022

• Hydrothermal_plume_omics_Zhou_et_al._2021

  Public
  Bioinformatic analyzing methods for hydrothermal plume omics paper

  Perl

  •

  Other

  •0•5•0•0•Updated May 6, 2022May 6, 2022

• Kieft_et_al_2021_organosulfur_AMGs

  Public
  1•0•0•0•Updated Apr 1, 2022Apr 1, 2022

• Kieft_and_Zhou_et_al._2020

  Public
  Perl

  •3•10•0•0•Updated Apr 1, 2022Apr 1, 2022

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •3.4k•0•0•0•Updated Sep 22, 2021Sep 22, 2021

• doden_et_al_2021

  Public
  0•0•0•0•Updated Feb 19, 2021Feb 19, 2021