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    26 repositories

    • ProtScout

      Public
      Filter protein sequences by predicted protein properties
      Python
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Jun 12, 2025Jun 12, 2025

    • veba

      Public
      A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. Built by @jolespin, stable maintenance and containerization from NewAtlantis
      Python
      •
      GNU Affero General Public License v3.0
      •10•3•0•0•Updated Jun 11, 2025Jun 11, 2025

    • ampliseq

      Public
      Amplicon sequencing analysis workflow using DADA2 and QIIME2
      Nextflow
      •
      MIT License
      •143•0•0•0•Updated Apr 14, 2025Apr 14, 2025

    • cgem-forge

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •1•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • Copernicus_downloader

      Public
      Tools to mass-download Copernicus time series data
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Mar 12, 2025Mar 12, 2025

    • ensemble_networkx

      Public
      Python package for association, differential, clustered, and sample-specific ensemble networks. Direct support for compositional data analysis. Additional capabilities for feature engineering.
      Python
      •
      Other
      •2•0•0•0•Updated Mar 5, 2025Mar 5, 2025

    • clairvoyance

      Public
      AutoML simultaneous bayesian hyperparameter optimization and feature selection
      Python
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Feb 20, 2025Feb 20, 2025

    • pyhmmsearch-stable

      Public
      Fast implementation of HMMSEARCH optimized for high-memory systems using PyHmmer
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 24, 2025Jan 24, 2025

    • Mg-Traits

      Public
      Shell
      •
      GNU General Public License v3.0
      •0•1•1•0•Updated Dec 27, 2024Dec 27, 2024

    • tiara-nal

      Public
      tiara – a tool for DNA sequence classification (NAL mod)
      Python
      •
      MIT License
      •10•0•0•3•Updated Dec 27, 2024Dec 27, 2024

    • metadecoder-nal

      Public
      An algorithm for clustering metagenomic sequences (NAL mod with Pyrodigal and PyHMMSearch)
      Python
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • metacoag-nal

      Public
      🚦🧬 Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs (NAL mod with Pyrodigal and PyHMMSearch)
      Python
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • hyena-postTrain-loop

      Public
      Jupyter Notebook
      •0•1•2•0•Updated Nov 15, 2024Nov 15, 2024

    • pykofamsearch-stable

      Public
      Fast implementation of KofamScan optimized for high-memory systems using PyHmmer
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 8, 2024Nov 8, 2024

    • kegg_pathway_profiler

      Public
      A pathway profiling tool designed for traversing metabolic pathway graphs, identifying most complete paths based on an evaluation set of KEGG orthologs (KO), and generalized for internal usage within Python and via CLI executables.
      Python
      •
      Apache License 2.0
      •1•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • na-erdos-fellows-monorepo

      Public
      The central location for code in the NewAtlantis fellowship program
      Jupyter Notebook
      •
      Apache License 2.0
      •21•3•0•1•Updated Aug 16, 2024Aug 16, 2024

    • comebin-nal

      Public
      Effective binning of metagenomic contigs using COntrastive Multi-viEw representation learning (NAL mod)
      Python
      •
      GNU General Public License v3.0
      •12•0•0•0•Updated Mar 10, 2024Mar 10, 2024

    • bioprospecting

      Public
      Jupyter Notebook
      •2•1•2•0•Updated Nov 24, 2023Nov 24, 2023

    • nal-notebook-templates

      Public
      a collection of notebook templates that are reflected on the cloud lab
      Jupyter Notebook
      •1•0•0•1•Updated Nov 2, 2023Nov 2, 2023

    • Living-Oceans

      Public
      🌊 Robust workflows for gathering data about your local ocean.
      pythonbioinformaticsmetagenomicspython3bioinformatics-pipelinemetagenomics-datametagenomics-toolkitjyputer-notebookdesci
      Jupyter Notebook
      •1•15•0•0•Updated Jul 19, 2023Jul 19, 2023

    • .github

      Public
      0•0•0•0•Updated Jun 20, 2023Jun 20, 2023

    • protocol-labs-demo

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Jun 7, 2023Jun 7, 2023

    • Metagenomics

      Public
      🐋 The Living Oceans Metagenome Taxanomic Profiling tool (beta) is a metagenomic pipeine built to work on your local ocean
      pythonbioinformaticsoceanmetagenomicspython3bioinformatics-pipelineplanktonmetagenomic-analysisgitcoinmetagenomic-pipeline
      Jupyter Notebook
      •
      Other
      •3•8•0•0•Updated Dec 18, 2022Dec 18, 2022

    • DiffDock_GPU_Stable

      Public
      Dockerized Version of the DiffDock model from MIT, Stable Release Maintained through NewAtlantis
      Jupyter Notebook
      •
      Apache License 2.0
      •4•0•0•0•Updated Dec 13, 2022Dec 13, 2022

    • presentations

      Public
      Materials notebooks for presentation/communications
      0•0•0•0•Updated Nov 10, 2022Nov 10, 2022

    • DeepLabCut

      Public
      Official implementation of DeepLabCut: Markerless pose estimation of user-defined features with deep learning for all animals incl. humans
      Python
      •
      GNU Lesser General Public License v3.0
      •1.7k•0•0•0•Updated Jul 29, 2022Jul 29, 2022