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@AnantharamanLab Anantharaman Microbiome Lab at UW-Madison

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    22 repositories

    • Clostridium_scindens_mining

      Public
      Shell
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Dec 11, 2024Dec 11, 2024

    • 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 Dec 9, 2024Dec 9, 2024

    • vClassifier

      Public
      Species-level taxonomic classification of viruses
      Shell
      •
      GNU General Public License v3.0
      •0•2•2•0•Updated Dec 6, 2024Dec 6, 2024

    • Prophage-DB

      Public
      Prophage-DB scripts for generating figures
      Jupyter Notebook
      •1•2•0•0•Updated Nov 15, 2024Nov 15, 2024

    • ViWrap

      Public
      A wrapper to identify, bin, classify, and predict host-viral relationship for viruses
      Python
      •15•67•28•1•Updated Oct 25, 2024Oct 25, 2024

    • ViromeVsMetagenome

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

    • V-Score-Search

      Public
      Searchable Database for V-Scores from VOG, PHROG, KEGG, eggNOG, and Pfam
      JavaScript
      •1•0•0•0•Updated Sep 3, 2024Sep 3, 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
      •0•0•0•0•Updated Apr 25, 2024Apr 25, 2024

    • VIBRANT

      Public
      Virus Identification By iteRative ANnoTation
      Python
      •
      GNU General Public License v3.0
      •38•154•48•1•Updated Apr 15, 2024Apr 15, 2024

    • Phage_T7

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

    • METABOLIC

      Public
      A scalable high-throughput metabolic and biogeochemical functional trait profiler
      Perl
      •45•183•109•1•Updated Jan 18, 2024Jan 18, 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•58•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•6•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
      •3.3k•0•0•0•Updated Sep 22, 2021Sep 22, 2021

    • doden_et_al_2021

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