maxplanck-ie/10X_snakepipe

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Python
Created over 6 years ago
Updated 3 months ago

maxplanck-ie/10X_snakepipe

maxplanck-ie

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A snakemake pipeline for 10X genomics cellranger

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...

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

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