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@maxplanck-ie Max Planck Institute of Immunobiology and Epigenetics

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    40 repositories

    • ATACofthesnake

      Public
      Differential accessibility, LRT tests and timecourse analyses for chromatin accessibility data
      atac-seqgaussian-processesatacseq
      atac-seqgaussian-processesatacseqmultifactorataclrttimecourse-analysistime-course
      Python
      •
      MIT License
      •2•3•0•0•Updated Apr 15, 2026Apr 15, 2026

    • snakepipes

      Public
      Customizable workflows based on snakemake and python for the analysis of NGS data
      workflowrna-seqsnakemake
      workflowrna-seqsnakemakengshi-cchip-seqatac-seqbisulfite-sequencing
      Python
      •90•404•29•3•Updated Apr 14, 2026Apr 14, 2026

    • parkour2

      Public
      Parkour2: Laboratory Information Management System 👩🏻‍🔬 🧬 👨🏽‍💻
      dockerdjangobioinformatics
      dockerdjangobioinformaticsvuelimsextjs
      Python
      •9•34•2•2•Updated Apr 13, 2026Apr 13, 2026

    • Rintro

      Public
      material for R-Course
      R
      •
      GNU General Public License v3.0
      •4•5•2•0•Updated Mar 20, 2026Mar 20, 2026

    • AlphaGenomeWorkshop

      Public
      Implementation of AlphaGenome API jupyter notebook.
      Jupyter Notebook
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • dissectBCL

      Public
      demultiplexing pipeline
      Python
      •2•1•19•1•Updated Feb 3, 2026Feb 3, 2026

    • nanoporeReads_dataTransfer

      Public
      A pipeline to transfer the Nanopore reads to end users
      Python
      •
      MIT License
      •3•0•2•1•Updated Jan 27, 2026Jan 27, 2026

    • oarfish_snakemake_workflow

      Public
      A snakemake workflow for standard and allele-specific DGE and DTE for ONT cDNA reads.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • chromHMM_snakemake_workflow

      Public
      A snakemake workflow to produce chromHMM segmentation on input bam files.
      Python
      •1•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • BigRedButton

      Public
      1. Push button 2. Get results 3. Publish
      Python
      •1•0•7•2•Updated Dec 9, 2025Dec 9, 2025

    • 10X_snakepipe

      Public
      A snakemake pipeline for 10X genomics cellranger
      Python
      •4•22•3•0•Updated Oct 13, 2025Oct 13, 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-genomics
      r-languageomicssingle-cell-genomicssingle-cell-rna-seqseurat
      R
      •
      GNU General Public License v3.0
      •0•5•1•0•Updated Jun 18, 2025Jun 18, 2025

    • pycoQC

      Public
      pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Gup…
      Python
      •
      GNU General Public License v3.0
      •41•0•0•0•Updated Oct 18, 2024Oct 18, 2024

    • HiCAssembler

      Public
      Software to assemble contigs/scaffolds into chromosomes using Hi-C data
      Python
      •4•28•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
      •16•0•0•1•Updated Jul 19, 2024Jul 19, 2024

    • snakequest

      Public
      A shiny app that collects user input required for running snakepipes.
      R
      •0•2•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•3•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•14•0•0•Updated Oct 7, 2022Oct 7, 2022

    • docker-galaxy-stable

      Public
      :whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
      Shell
      •
      MIT License
      •139•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
      lims
      JavaScript
      •
      GNU General Public License v3.0
      •15•32•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
      •3•2•1•0•Updated Jun 15, 2021Jun 15, 2021
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