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    32 repositories

    • strain_tracking

      Public
      Code for pregnancy and mother-infact strain tracking project
      Jupyter Notebook
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • 232_FOCUS

      Public
      Analyses related to the FOCUS/Oncobiome projects (232 OncDutch)
      Python
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • rstudio_singularity

      Public
      Run Rstudio with Singularity
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 13, 2025Jun 13, 2025

    • crc-survival

      Public
      Code for Tumor Microbiome is associated with survival in late stage colorectal cancer
      Jupyter Notebook
      •1•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • ML_swemami

      Public
      Machine learning code used for SweMaMi study on miscarriage
      0•1•0•0•Updated Oct 1, 2024Oct 1, 2024

    • valody

      Public
      A tool to assign VAginaL DYnamic categories to individuals based on their Valencia CST assignments
      Python
      •
      MIT License
      •1•2•0•0•Updated Sep 30, 2024Sep 30, 2024

    • stag-mwc

      Public
      StaG Metagenomic Workflow Collaboration
      researchmetagenomicsmicrobiomemetagenomic-analysissnakemake-workflows
      Python
      •
      MIT License
      •13•28•4•1•Updated Aug 20, 2024Aug 20, 2024

    • ENA_submission_notebooks

      Public
      Notebooks in Jupyter that can be used for filling out meta data checklists required for uploading data to the ENA
      Jupyter Notebook
      •0•0•0•0•Updated Apr 12, 2024Apr 12, 2024

    • 194_BOuru_shotgun_analysis

      Public
      0•0•0•0•Updated Nov 30, 2023Nov 30, 2023

    • slurm-jobstats

      Public
      Compute job statistics for Slurm jobs
      Python
      •
      MIT License
      •0•2•0•0•Updated Nov 7, 2023Nov 7, 2023

    • sm3

      Public
      Simple Snakemake example
      Python
      •
      MIT License
      •0•1•0•0•Updated May 2, 2023May 2, 2023

    • ctmr-superset

      Public
      Custom Docker image for Apache Superset
      Shell
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 25, 2023Apr 25, 2023

    • gitdemo

      Public
      0•0•0•0•Updated Apr 20, 2023Apr 20, 2023

    • s3etag

      Public
      Compute ETag of local file and compare to file on S3
      Python
      •0•0•0•0•Updated Feb 2, 2023Feb 2, 2023

    • bioinformatics_curriculum

      Public
      Some ideas on things to learn to get started with bioinformatics
      MIT License
      •7•19•1•0•Updated Dec 5, 2022Dec 5, 2022

    • sourmash_sketch

      Public
      Compare samples based on kmers using Sourmash sketch
      Nextflow
      •
      MIT License
      •0•1•0•0•Updated Sep 13, 2022Sep 13, 2022

    • claritylims

      Public
      Customizations for our GenoLogics BaseSpace Clarity LIMS
      lims
      Python
      •
      MIT License
      •2•2•17•2•Updated Jul 8, 2022Jul 8, 2022

    • pseudomonas_boanensis_db1

      Public
      comparative genomic analysis for Pseudomonas boanensis DB1
      Jupyter Notebook
      •0•0•0•0•Updated Mar 14, 2022Mar 14, 2022

    • run_in_parallel

      Public
      Run simple commands in parallel on Slurm
      Python
      •
      MIT License
      •0•0•4•0•Updated Feb 11, 2022Feb 11, 2022

    • Salgae_c-di-GMP_analysis

      Public
      Minhash/pangenome analysis notebooks and associated files
      Jupyter Notebook
      •1•0•0•0•Updated Jan 5, 2022Jan 5, 2022

    • ctmr_lab_interface

      Public
      Scripts used to facilitate the interface between bioinformatic and experimental microbiology
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Dec 17, 2021Dec 17, 2021

    • optivag

      Public
      Database for annotating vaginal communities
      Python
      •
      MIT License
      •2•1•0•0•Updated Oct 8, 2021Oct 8, 2021

    • print_ctmr_labels

      Public
      Print CTMR labels on Zebra printer
      Python
      •0•2•4•1•Updated May 21, 2021May 21, 2021

    • estimate_seq_depth_notebooks

      Public
      Notebooks for the estimate_seq_depth project
      Jupyter Notebook
      •0•0•0•0•Updated May 20, 2021May 20, 2021

    • SARS-CoV-2_Multi-PCR_v1.0

      Public
      SARS-CoV-2 analysis pipeline for multiplex-PCR MPS(Massive Parrallel Sequencing) data
      Perl
      •11•0•0•0•Updated May 18, 2021May 18, 2021

    • BVAB-and-Lac-sequences

      Public
      The database contains a collection of sequences for BVAB (Bacterial vaginosis associated bacteria) and common vaginal Lactobacillus species.
      0•1•0•0•Updated Jul 5, 2020Jul 5, 2020

    • Zebra_GK420t

      Public
      Script for printing labels on Zebra GK420t
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 11, 2020Jun 11, 2020

    • mgi-ncov19-snakemake

      Public
      Python
      •1•0•0•0•Updated Apr 14, 2020Apr 14, 2020

    • dockerfiles

      Public archive
      Dockerfiles used at CTMR
      Dockerfile
      •
      MIT License
      •0•0•2•1•Updated Mar 29, 2019Mar 29, 2019

    • Amplicon_workflows

      Public
      Workflows and scripts for amplicon sequencing processing
      Python
      •1•1•0•0•Updated Jan 24, 2019Jan 24, 2019