Pinned Repositories
Bio-Toolbox
A loose collection of mixins and libs, packaged as a gem
clinical-metagenomics
eutaxpro
Taxonomic profiling of eukaroyte genomes using amplicon sequencing
expression-database
gabi
Genomic Analysis of Bacterial Isolates
genome-database
MYSQL-based genome database template
genomeannotator
gmo-check
Pipeline to check GMOs from short read data
nf-configs
Centrally managed configuration profiles for various pipelines
nf-template
A template for a creating a new nextflow pipeline project.
marchoeppner's Repositories
marchoeppner/genomeannotator
marchoeppner/gabi
Genomic Analysis of Bacterial Isolates
marchoeppner/ikmb_amplicon_processing
marchoeppner/metaorganism-research
Production pipelines for the CRC1182
marchoeppner/nf-configs
Centrally managed configuration profiles for various pipelines
marchoeppner/configs
Config files used to define parameters specific to compute environments at different Institutions.
marchoeppner/eutaxpro
Taxonomic profiling of eukaroyte genomes using amplicon sequencing
marchoeppner/exome-seq
marchoeppner/gmo-check
Pipeline to check GMOs from short read data
marchoeppner/metagenomic-profiling
marchoeppner/nf-template
A template for a creating a new nextflow pipeline project.
marchoeppner/ngs-qc
QC tools for new sequencing runs (FastQC, FastQ Screen, MultiQC Report)
marchoeppner/Augustus
Genome annotation with AUGUSTUS
marchoeppner/augustus-container
Containerize Augustus ComPred
marchoeppner/BloodTypingArray
The software for the Intitutes genotyping array based blood group typing
marchoeppner/LaMeta
LaMeta - getting more from your metagenomic data (like you used to...)
marchoeppner/ncrna-annotation
Annotate ncRNAs from assemblies using Rfam
marchoeppner/nf-flu
Influenza genome analysis Nextflow workflow
marchoeppner/nf-mlst
Perform (cg)MLST on a set of bacterial genome assemblies
marchoeppner/nf-testdata
Test datasets for nextflow pipeline
marchoeppner/ngs-dm
marchoeppner/pathoscope2-docker
Instructions for a docker container with pathoscope2
marchoeppner/read-qc
NGS read qc
marchoeppner/sanger-profile
Profile amplicons from Sanger sequencing with optional assembly
marchoeppner/sanger-taxonomy
Taxonomic profiling of Sanger amplicons
marchoeppner/SatsumaKraken
Build instructions for Satsuma2+ Kraken Docker container
marchoeppner/scripts
Collection of various scripts
marchoeppner/taxidtools
Python library to deal with taxonomic IDs and lineages from the NCBI's Taxdump files
marchoeppner/test-datasets
Test data to be used for automated testing with the nf-core pipelines
marchoeppner/VEP_plugins
Plugins for the Ensembl Variant Effect Predictor (VEP)