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    37 repositories

    • parkour2

      Public
      Parkour2: Laboratory Information Management System 👩🏻‍🔬 🧬 👨🏽‍💻
      dockerdjangobioinformaticsvuelimsextjs
      Python
      •8•32•0•3•Updated Aug 14, 2025Aug 14, 2025

    • nanoporeReads_dataTransfer

      Public
      A pipeline to transfer the Nanopore reads to end users
      Python
      •
      MIT License
      •3•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • BigRedButton

      Public
      1. Push button 2. Get results 3. Publish
      Python
      •1•0•5•1•Updated Aug 12, 2025Aug 12, 2025

    • snakepipes

      Public
      Customizable workflows based on snakemake and python for the analysis of NGS data
      workflowrna-seqsnakemakengshi-cchip-seqatac-seqbisulfite-sequencing
      Python
      •89•398•43•2•Updated Aug 11, 2025Aug 11, 2025

    • ATACofthesnake

      Public
      Differential accessibility calculation for bulk-ATAC seq.
      atacseqatac
      Python
      •
      MIT License
      •1•2•9•0•Updated Aug 2, 2025Aug 2, 2025

    • dissectBCL

      Public
      demultiplexing pipeline
      Python
      •2•1•18•0•Updated Jul 29, 2025Jul 29, 2025

    • customcontamination

      Public
      a list of custom contaminants.
      2•0•0•0•Updated Jul 24, 2025Jul 24, 2025

    • Rdeseq2

      Public
      Material for the advanced R course
      R
      •0•1•1•0•Updated Jun 25, 2025Jun 25, 2025

    • Rseurat

      Public
      Single Cell RNA-seq Course
      r-languageomicssingle-cell-genomicssingle-cell-rna-seqseurat
      R
      •
      GNU General Public License v3.0
      •0•4•1•0•Updated Jun 18, 2025Jun 18, 2025

    • Rintro

      Public
      material for R-Course
      R
      •
      GNU General Public License v3.0
      •3•5•2•0•Updated Mar 31, 2025Mar 31, 2025

    • 10X_snakepipe

      Public
      A snakemake pipeline for 10X genomics cellranger
      Python
      •4•21•3•0•Updated Dec 19, 2024Dec 19, 2024

    • pycoQC

      Public
      pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
      Python
      •
      GNU General Public License v3.0
      •40•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • HiCAssembler

      Public
      Software to assemble contigs/scaffolds into chromosomes using Hi-C data
      Python
      •4•29•19•0•Updated Sep 26, 2024Sep 26, 2024

    • Pore-C-Snakemake

      Public
      Fork of Pore-C-Snakemake for running on the MPI cluster
      Python
      •
      Other
      •15•0•0•1•Updated Jul 19, 2024Jul 19, 2024

    • snakequest

      Public
      A shiny app that collects user input required for running snakepipes.
      R
      •0•3•0•0•Updated Jun 13, 2024Jun 13, 2024

    • ultraheatmap

      Public
      extra pumped heatmaps
      Python
      •
      MIT License
      •2•3•2•0•Updated Feb 13, 2024Feb 13, 2024

    • sc-VirusScan

      Public
      A Snakemake pipeline for identifying viruses from single-cell data.
      Python
      •1•2•4•0•Updated Jan 30, 2024Jan 30, 2024

    • nextflow_hackathon

      Public
      Nextflow
      •2•0•1•0•Updated Nov 28, 2023Nov 28, 2023

    • mpi-ie-slurm

      Public
      A simple Snakemake profile for Slurm without --cluster-config
      Shell
      •
      Creative Commons Zero v1.0 Universal
      •19•0•0•0•Updated Oct 14, 2022Oct 14, 2022

    • cookiecutter-bioinformatics-project

      Public
      A cookiecutter template for bioinformatics projects, inspired by cookiecutter-data-science and Snakemake Workflows.
      Python
      •
      MIT License
      •3•11•0•0•Updated Oct 7, 2022Oct 7, 2022

    • docker-galaxy-stable

      Public
      🐳📊📚 Docker Images tracking the stable Galaxy releases.
      Shell
      •
      MIT License
      •136•1•0•1•Updated Sep 28, 2022Sep 28, 2022

    • TheWhoTheWhatTheHuh

      Public archive
      "The who the what the huh?" is our pipeline for converting bcl files to fastq and performing QC.
      Python
      •2•11•2•0•Updated Sep 19, 2022Sep 19, 2022

    • parkour

      Public archive
      Moved to: https://github.com/maxplanck-ie/parkour2
      lims
      JavaScript
      •
      GNU General Public License v3.0
      •14•34•12•2•Updated Aug 24, 2022Aug 24, 2022

    • docker-parkour

      Public archive
      Moved to: https://github.com/maxplanck-ie/parkour2
      Dockerfile
      •2•0•1•0•Updated Jul 11, 2022Jul 11, 2022

    • TRAP

      Public
      tools and utilities for annotating DNA sequences
      Perl
      •
      GNU General Public License v3.0
      •1•1•0•1•Updated Nov 30, 2021Nov 30, 2021

    • bulkRNAseq_MPI_shiny_app

      Public
      Takes feature counts output and plots heatmaps and barplots for selected genes.
      HTML
      •0•0•0•0•Updated Nov 19, 2021Nov 19, 2021

    • Genes2Functions

      Public
      This is a shiny app built around clusterProfiler to perform functional enrichment analysis from RNA-Seq DE analysis
      HTML
      •2•1•1•0•Updated Jun 15, 2021Jun 15, 2021

    • DGE-viz

      Public
      Upload your DGE (differential gene expression) table and visually select gene sets
      R
      •2•0•1•0•Updated Feb 15, 2021Feb 15, 2021

    • MPI_shiny_landing_page

      Public
      The landing page for MPI-IE shiny apps.
      HTML
      •0•0•0•0•Updated Jan 25, 2021Jan 25, 2021

    • docker-blast

      Public
      wwwblast in a docker container
      Dockerfile
      •0•1•0•0•Updated Sep 23, 2020Sep 23, 2020