Stars
Teaching material for the MPUSP Python + R course for beginners
Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.
Information and stats about the MPUSP bioinformatics platform.
A helper program that extracts the input and output filenames from rules in snakemake workflow
An awesome tool to visualize snakemake rule graphs
Resuable CI workflows for our snakemake pipelines
streamlined singularity python client (spython) for singularity
Random selection of useful code chunks and examples for bioinformatics
A Github action for running a Snakemake workflow
A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.
Custom wrappers for recurring MPUSP Snakemake rules
Pipeline for automatic processing and quality control of mass spectrometry data
A standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing data
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
A template for standard compliant snakemake-workflows
A Snakemake workflow for basecalling and demultiplexing of Oxford Nanopore data using Dorado.
This is the development home of the Snakemake wrapper repository, see
Transcript assembly and quantification for RNA-Seq
A Snakemake workflow for the processing of short read rnaseq data in bacteria.
A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.
R package to Import and Modify SVG (XML) Graphic Files
Updated FlaGs version. Replaces tkinter module for matplotlib for the graphical output.
An R package implementing the UMAP dimensionality reduction method.
A statically generated catalog of available Snakemake workflows
Visualize and annotate genomic coverage with ggplot2
GEKKO Python for Machine Learning and Dynamic Optimization
Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.