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    118 repositories

    • pankb_data_prep

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • pankb_db

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • dsp_nextflow_training

      Public
      Hands-on Nextflow training materials and information
      nextflow
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

    • pankb_llm

      Public
      An LLM-based pangenomics chatbot integrated into the PanKB website.
      mongodbazurechatbotpangenomicscosmosdbstreamlitllmvectordbgenai
      Python
      •0•0•0•0•Updated Oct 10, 2024Oct 10, 2024

    • pankb

      Public
      The Pangenome Knowledge Base (PanKB) serves as an up-to-date resource for pangenomics research methods and the dissemination of results and currently offers basic pangenome characteristics and advanced pangenome analytics for 8 major biotech bacteria families.
      HTML
      •
      MIT License
      •0•1•0•0•Updated Oct 10, 2024Oct 10, 2024

    • dsp_workshop_datavizR

      Public
      Introduction to Data Visualization: Theory and practice using R
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • notes_template

      Public template
      Notes template build on Sphinx, Myst parser and a template
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • dsp_notes_template_test

      Public
      Example template testing for course
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • Alleleome

      Public
      Tools to generate core- and panalleleomes.
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • dsp_pandas

      Public
      Organize pandas based functionality across projects.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • snakemake-ont-bacterial-variants

      Public
      A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.
      Python
      •
      Other
      •1•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • dsp_notes

      Public
      Public notes and hints of the Data Science Platform.
      Jupyter Notebook
      •1•1•0•0•Updated Sep 23, 2024Sep 23, 2024

    • simplified_data_science_project_template

      Public template
      A template for data science projects. Simplified, based on datadriven.org's cookiecutter.
      Other
      •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • Growth-coupling-suite

      Public
      A constraint-based metabolic model-based workflow for computing and analyzing microbial strain design which couple a target reaction to growth
      Python
      •
      MIT License
      •1•3•1•0•Updated Sep 17, 2024Sep 17, 2024

    • dsp_nfcore_taxprofiler

      Public
      Taxonomica profiling using nf-core/taxprofiler pipeline
      Nextflow
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • Maud

      Public
      Enzyme models that take into account kinetics, allostery and thermodynamics
      Python
      •
      GNU General Public License v3.0
      •2•26•22•2•Updated Sep 3, 2024Sep 3, 2024

    • salb_imodulons

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 25, 2024Aug 25, 2024

    • ESS-Designs

      Public
      HTML
      •
      MIT License
      •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

    • code-quality-check

      Public
      0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • shu

      Public
      Multi-dimensional, trans-omics metabolic maps.
      visualizationsystems-biologymetabolism
      Rust
      •
      Apache License 2.0
      •1•44•7•1•Updated Aug 19, 2024Aug 19, 2024

    • dsp_nfcore-nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •80•0•0•0•Updated Aug 13, 2024Aug 13, 2024

    • nanoseq

      Public
      Nanopore demultiplexing, QC and alignment pipeline
      Nextflow
      •
      MIT License
      •80•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • incawrapper

      Public
      A python wrapper for Metabolic Flux Analysis (MFA) using INCA with additional functionalities
      fluxmetabolismmodeling
      Python
      •
      MIT License
      •0•3•1•0•Updated Jul 2, 2024Jul 2, 2024

    • pseudobatch

      Public
      The Pseudobatch transformation is a method to easy analysis of measurement from a fed-batch fermentation process. After transformation, the data can be analysed as if it was obtained from a batch fermentation process. The Pseudobatch transformation is especially useful for fed-batch processes where samples where drawn from the bioreactor.
      microbiologyfermentationfermentation-processfed-batch
      Jupyter Notebook
      •
      MIT License
      •0•5•3•0•Updated Jun 20, 2024Jun 20, 2024

    • datacatalog-documentation

      Public
      0•2•1•0•Updated Jun 6, 2024Jun 6, 2024

    • dgfreg

      Public
      Regression models of biochemical formation energies
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jun 6, 2024Jun 6, 2024

    • dsp_nf-metagenomics

      Public
      Shotgun metagenomics pipeline to process microbiome samples
      metagenomicsnextflow-pipeline
      Shell
      •
      GNU General Public License v3.0
      •0•3•2•0•Updated Jun 6, 2024Jun 6, 2024

    • msdap

      Public
      MS-DAP: downstream analysis pipeline for quantitative proteomics
      R
      •
      GNU General Public License v3.0
      •7•0•0•0•Updated Jun 3, 2024Jun 3, 2024

    • dsp_nf-msdap

      Public
      Nextflow pipeline for MS-DAP, a downstream pipeline to generate statistical reports for MS data
      proteomicsdownstream-analysisnextflow-pipeline
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 31, 2024May 31, 2024

    • GEM-Exometabolome

      Public
      Pipeline for the integration of exometabolomic data into GEM analysis and interpretation
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated May 23, 2024May 23, 2024