Max Planck Institute of Immunobiology and Epigenetics's repositories
snakepipes
Customizable workflows based on snakemake and python for the analysis of NGS data
HiCAssembler
Software to assemble contigs/scaffolds into chromosomes using Hi-C data
10X_snakepipe
A snakemake pipeline for 10X genomics cellranger
TheWhoTheWhatTheHuh
"The who the what the huh?" is our pipeline for converting bcl files to fastq and performing QC.
cookiecutter-bioinformatics-project
A cookiecutter template for bioinformatics projects, inspired by cookiecutter-data-science and Snakemake Workflows.
data_repository
Makefiles and all associated scripts needed to completely remake /data/repository on all linux desktops
snakequest
A shiny app that collects user input required for running snakepipes.
ultraheatmap
extra pumped heatmaps
ATACofthesnake
Differential accessibility calculation for bulk-ATAC seq.
sc-VirusScan
A Snakemake pipeline for identifying viruses from single-cell data.
docker-blast
wwwblast in a docker container
docker-galaxy-stable
:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
Genes2Functions
This is a shiny app built around clusterProfiler to perform functional enrichment analysis from RNA-Seq DE analysis
dissectBCL
demultiplexing pipeline
BigRedButton
1. Push button 2. Get results 3. Publish
bulkRNAseq_MPI_shiny_app
Takes feature counts output and plots heatmaps and barplots for selected genes.
docker-parkour
Moved to: https://github.com/maxplanck-ie/parkour2
mpi-ie-slurm
A simple Snakemake profile for Slurm without --cluster-config
MPI_shiny_landing_page
The landing page for MPI-IE shiny apps.
nanoporeReads_dataTransfer
A pipeline to transfer the Nanopore reads to end users
Pore-C-Snakemake
Fork of Pore-C-Snakemake for running on the MPI cluster