maxplanck-ie/TheWhoTheWhatTheHuh

This repository has been archived on 19/Sep/2022
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Created over 9 years ago
Updated about 2 years ago

maxplanck-ie/TheWhoTheWhatTheHuh

maxplanck-ie

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"The who the what the huh?" is our pipeline for converting bcl files to fastq and performing QC.

snakepipes

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

parkour

Moved to: https://github.com/maxplanck-ie/parkour2

HiCAssembler

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

parkour2

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

rna-seq-qc

Rna-seq pipeline, From FASTQ to differential expression analysis...

10X_snakepipe

A snakemake pipeline for 10X genomics cellranger

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

Rintro

material for R-Course

Rseurat

Single Cell RNA-seq Course

snakequest

A shiny app that collects user input required for running snakepipes.

ultraheatmap

extra pumped heatmaps

sc-VirusScan

A Snakemake pipeline for identifying viruses from single-cell data.

ATACofthesnake

Differential accessibility calculation for bulk-ATAC seq.

Misc

Miscellaneous file that should probably be version controlled, but don't really need their own repositories.

docker-blast

wwwblast in a docker container

TRAP

tools and utilities for annotating DNA sequences

Rdeseq2

Material for the advanced R course

Genes2Functions

This is a shiny app built around clusterProfiler to perform functional enrichment analysis from RNA-Seq DE analysis

dissectBCL

demultiplexing pipeline