Repositories list

• parkour2

  Public
  Parkour2: Laboratory Information Management System 👩🏻‍🔬 🧬 👨🏽‍💻

  pythonapidocker+ 9djangobioinformaticssqlvuelimswebappextjs+ 2

  Python

  •6•26•0•1•Updated Oct 23, 2024Oct 23, 2024

• snakepipes

  Public
  Customizable workflows based on snakemake and python for the analysis of NGS data

  workflowrna-seqsnakemake+ 5ngshi-cchip-seqatac-seqbisulfite-sequencing

  Python

  •85•382•41•1•Updated Oct 22, 2024Oct 22, 2024

• BigRedButton

  Public
  1. Push button 2. Get results 3. Publish

  Python

  •0•0•1•1•Updated Oct 17, 2024Oct 17, 2024

• nanoporeReads_dataTransfer

  Public
  A pipeline to transfer the Nanopore reads to end users

  Python

  •

  MIT License

  •4•0•19•0•Updated Oct 16, 2024Oct 16, 2024

• 10X_snakepipe

  Public
  A snakemake pipeline for 10X genomics cellranger

  Python

  •4•19•0•0•Updated Oct 7, 2024Oct 7, 2024

• HiCAssembler

  Public
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data

  Python

  •4•27•18•0•Updated Sep 26, 2024Sep 26, 2024

• Rseurat

  Public
  Single Cell RNA-seq Course

  r-languageomicssingle-cell-genomics+ 2single-cell-rna-seqseurat

  R

  •

  GNU General Public License v3.0

  •0•3•1•0•Updated Sep 18, 2024Sep 18, 2024

• dissectBCL

  Public
  demultiplexing pipeline

  Python

  •1•1•9•0•Updated Aug 26, 2024Aug 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

• Rdeseq2

  Public
  Material for the advanced R course

  R

  •0•1•4•0•Updated May 25, 2024May 25, 2024

• Rintro

  Public
  material for R-Course

  R

  •

  GNU General Public License v3.0

  •3•4•2•0•Updated Apr 22, 2024Apr 22, 2024

• ATACofthesnake

  Public
  Differential accessibility calculation for bulk-ATAC seq.

  atacseqatac

  Python

  •

  MIT License

  •1•2•9•0•Updated Apr 9, 2024Apr 9, 2024

• ultraheatmap

  Public
  extra pumped heatmaps

  Python

  •

  MIT License

  •1•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

  •18•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•8•0•0•Updated Oct 7, 2022Oct 7, 2022

• docker-galaxy-stable

  Public
  🐳📊📚 Docker Images tracking the stable Galaxy releases.

  Shell

  •

  MIT License

  •133•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

  •15•33•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

  •1•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

• scRNAseq_shiny_app

  Public
  HTML

  •

  GNU General Public License v3.0

  •0•0•3•0•Updated Aug 25, 2020Aug 25, 2020

• data_repository

  Public
  Makefiles and all associated scripts needed to completely remake /data/repository on all linux desktops

  Makefile

  •1•4•0•0•Updated Jan 28, 2020Jan 28, 2020