holtgrewe
Data + Transistors => biomedical insight (and everything in between) @bihealth
CUBI Core Unit Bioinformatics, Berlin Institute of HealthBerlin
Pinned Repositories
cnvetti
:tada: CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data
hlama
Simple matching of HTS samples based on HLA typing
vcfpy
Python 3 library with good support for both reading and writing VCF
jannovar
Annotation of VCF variants with functional impact and from databases (executable+library)
linty
C++ convention/style checker in Python using libclang.
mason3
Mason read simulator version 3 (with 100% more emojis and Rust)
ngs_pipelines
Nextflow-based pipelines for typical NGS processing tasks
seqan
SeqAn's official repository.
varfish-server
VarFish: comprehensive DNA variant analysis for diagnostics and research
holtgrewe's Repositories
holtgrewe/mason3
Mason read simulator version 3 (with 100% more emojis and Rust)
holtgrewe/holtgrewe.github.io
Full-stack Bioinformatics (my blog - I'm so 00s')
holtgrewe/bioconda-recipes
Conda recipes for the bioconda channel.
holtgrewe/dotfiles
holtgrewe/hgvs
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
holtgrewe/alertmanager
Prometheus Alertmanager
holtgrewe/biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
holtgrewe/CADA
holtgrewe/cdot
Transcript versions for HGVS libraries
holtgrewe/checkmk
Checkmk - Best-in-class infrastructure & application monitoring
holtgrewe/dash-dwd
holtgrewe/drf-pydantic
Use pydantic with the Django REST framework
holtgrewe/haplotype-lso
Haplotyping of C. Liberibacter solanacearum from Sanger data
holtgrewe/holtgrewe
Profile README
holtgrewe/hpo
Rust library for the Human Phenotype Ontology
holtgrewe/inline-html
Python script for inlining CSS stylesheets and conversion of resources to data-uri
holtgrewe/kayobe-config
Configuration files for kayobe. Mirror of code maintained at opendev.org.
holtgrewe/manuelholtgrewe.de
holtgrewe/mwp-rust-rocksdb-cache
holtgrewe/noodles
Bioinformatics I/O libraries in Rust
holtgrewe/pb-human-wgs-workflow-snakemake
Workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads
holtgrewe/rust-rocksdb
rust wrapper for rocksdb
holtgrewe/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
holtgrewe/snakemake-profiles-slurm
Cookiecutter for snakemake slurm profile
holtgrewe/snapshottest
Snapshot Testing utils for Python 📸
holtgrewe/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
holtgrewe/tensorflow-feedstock
A conda-smithy repository for tensorflow.
holtgrewe/uta
Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image
holtgrewe/vuetify3-vue3-test
Example of using vue3/vuetify3 with unit tests
holtgrewe/wthr-server
Weather data sink and dashboard (Flask+Plotly Dash)