Labor Berlin - Charité Vivantes GmbH
Clinical Plattform "Bioinformatics & Data Science"
Berlin, Germany
Pinned Repositories
hum-cubi-tk-fork
CUBI Tooling for SODAR, VarFish et al.
hum-exomiser-fork
A Tool to Annotate and Prioritize Exome Variants
hum-varfish-cli-fork
VarFish REST API client (CLI + Python package)
hum-varfish-server-fork
VarFish: comprehensive DNA variant analysis for diagnostics and research
LB-ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
ont-assembly-snake
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
varvis-download
A CLI tool to download genomic analysis files from the Varvis API. Supports authentication, file type selection, proxy settings, and destination directory specification.
Labor Berlin - Charité Vivantes GmbH's Repositories
LaborBerlin/score-assemblies
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
LaborBerlin/ont-assembly-snake
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
LaborBerlin/hum-exomiser-fork
A Tool to Annotate and Prioritize Exome Variants
LaborBerlin/LB-ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
LaborBerlin/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
LaborBerlin/varvis-download
A CLI tool to download genomic analysis files from the Varvis API. Supports authentication, file type selection, proxy settings, and destination directory specification.
LaborBerlin/bioconda-recipes
Conda recipes for the bioconda channel.
LaborBerlin/chatgpt-mattermost-bot
A very simple implementation of a service for a mattermost bot that uses ChatGPT in the backend.
LaborBerlin/hum-cubi-tk-fork
CUBI Tooling for SODAR, VarFish et al.
LaborBerlin/hum-gene-ranking-shootout
A small benchmark for comparing gene ranking methods
LaborBerlin/hum-varfish-annotator-fork
Annotate variants for import into VarFish server.
LaborBerlin/hum-varfish-cli-fork
VarFish REST API client (CLI + Python package)
LaborBerlin/hum-varfish-db-downloader-fork
Download public/static databases for VarFish
LaborBerlin/hum-varfish-docker-compose-fork
Setup VarFish as using Docker Compose
LaborBerlin/hum-varfish-server-fork
VarFish: comprehensive DNA variant analysis for diagnostics and research
LaborBerlin/LB-tbdb
Standard database for the TBProfiler tool
LaborBerlin/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
LaborBerlin/scramble
LaborBerlin/TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
LaborBerlin/hum-ngs-vntyper
A tool to genotype MUC1 coding VNTR in ADTKD