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    133 repositories

    • germinal

      Public
      Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.
      Python
      •
      Apache License 2.0
      •45•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • NVFlare

      Public
      NVIDIA Federated Learning Application Runtime Environment
      Python
      •
      Apache License 2.0
      •266•0•0•0•Updated Oct 3, 2025Oct 3, 2025

    • MemMachine

      Public
      Universal memory layer for AI Agents. It provides scalable, extensible, and interoperable memory storage and retrieval to streamline AI agent state management f…
      Python
      •
      Apache License 2.0
      •195•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • rosetta

      Public
      The Rosetta Bio-macromolecule modeling package.
      C++
      •
      Other
      •163•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • nvMolKit

      Public
      A high-performance, GPU-accelerated library for key computational chemistry tasks, such as molecular similarity, conformer generation, and geometry relaxation.
      Cuda
      •26•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • RFdiffusion

      Public
      Code for running RFdiffusion
      Python
      •
      Other
      •631•0•0•0•Updated Sep 24, 2025Sep 24, 2025

    • la-proteina

      Public
      A partially latent flow matching model for the joint generation of a protein’s amino acid sequence and full atomistic structure, including both the backbone and…
      Python
      •37•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • ReaSyn

      Public
      ReaSyn is a model for predicting a molecule's synthesis pathway, reaction steps from building blocks to final product(s), using an encoder-decoder Transformer a…
      Python
      •
      Apache License 2.0
      •16•0•0•0•Updated Sep 23, 2025Sep 23, 2025

    • RFdiffusion2

      Public
      Inference code for RFdiffusion2
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •69•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • proteina

      Public
      Proteina is a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scala…
      Python
      •
      Other
      •38•0•0•0•Updated Jul 24, 2025Jul 24, 2025

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •1.1k•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • rnaseq

      Public
      RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
      Nextflow
      •
      MIT License
      •881•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •223•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • epitopeprediction

      Public
      A bioinformatics best-practice analysis pipeline for epitope prediction and annotation
      Nextflow
      •
      MIT License
      •34•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • tools

      Public
      Python package with helper tools for the nf-core community.
      Python
      •
      MIT License
      •250•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • datasync

      Public
      nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks
      Nextflow
      •
      MIT License
      •8•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • riboseq

      Public
      Pipeline for the analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting) data.
      Nextflow
      •
      MIT License
      •21•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • website

      Public
      Code and files for the main nf-core website.
      Astro
      •
      MIT License
      •296•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      •
      MIT License
      •539•0•0•0•Updated Feb 26, 2024Feb 26, 2024

    • vscode-extensionpack

      Public
      A VSCode extension pack for nf-core developers.
      MIT License
      •5•0•0•0•Updated Feb 25, 2024Feb 25, 2024

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •366•0•0•0•Updated Feb 25, 2024Feb 25, 2024

    • mhcquant

      Public
      Identify and quantify MHC eluted peptides from mass spectrometry raw data
      Nextflow
      •
      MIT License
      •34•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •521•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • mag

      Public
      Assembly and binning of metagenomes
      Nextflow
      •
      MIT License
      •154•0•0•0•Updated Feb 24, 2024Feb 24, 2024

    • methylseq

      Public
      Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
      Nextflow
      •
      MIT License
      •175•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • variantbenchmarking

      Public
      A nextflow variant benchmarking pipeline - premature
      Nextflow
      •
      MIT License
      •30•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • pangenome

      Public
      Renders a collection of sequences into a pangenome graph.
      Nextflow
      •
      MIT License
      •22•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • AzureTRE

      Public
      An accelerator to help organizations build Trusted Research Environments on Azure.
      Python
      •
      MIT License
      •185•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • differentialabundance

      Public
      Differential abundance analysis for feature/ observation matrices from platforms such as RNA-seq
      Nextflow
      •
      MIT License
      •62•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • smrnaseq

      Public
      A small-RNA sequencing analysis pipeline
      Nextflow
      •
      MIT License
      •134•0•0•0•Updated Feb 23, 2024Feb 23, 2024
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