Labor Berlin - Charité Vivantes GmbH

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21 repositories

bedrock-claude-chat
Public
AWS-native chatbot using Bedrock + Claude (+Mistral)
TypeScript
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MIT No Attribution
•328•0•0•0•Updated Nov 28, 2024Nov 28, 2024
varvis-download
Public
A CLI tool to download genomic analysis files from the Varvis API. Supports authentication, file type selection, proxy settings, and destination directory specification.
api cli node bioinformatics authentication genomics proxy-support data-download varvis
JavaScript
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GNU General Public License v3.0
•0•1•3•0•Updated Oct 18, 2024Oct 18, 2024
chatgpt-mattermost-bot
Public
A very simple implementation of a service for a mattermost bot that uses ChatGPT in the backend.
TypeScript
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MIT License
•48•0•0•0•Updated Oct 16, 2024Oct 16, 2024
hum-exomiser-fork
Public
A Tool to Annotate and Prioritize Exome Variants
Java
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GNU Affero General Public License v3.0
•55•1•0•0•Updated Sep 20, 2024Sep 20, 2024
hum-ngs-vntyper
Public
A tool to genotype MUC1 coding VNTR in ADTKD
Python
•4•0•0•0•Updated May 31, 2024May 31, 2024
LB-tbdb
Public
Standard database for the TBProfiler tool
Python
•
GNU Lesser General Public License v3.0
•18•0•0•0•Updated May 13, 2024May 13, 2024
ont-assembly-snake
Public
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.
Python
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MIT License
•2•18•0•0•Updated Apr 23, 2024Apr 23, 2024
score-assemblies
Public
Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).
bioinformatics genome-analysis genome-assembly nanopore-sequencing snakemake-pipeline bacterial-genome-analysis nanopore-assembly
Python
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MIT License
•1•24•0•0•Updated Apr 5, 2024Apr 5, 2024
hum-cubi-tk-fork
Public
CUBI Tooling for SODAR, VarFish et al.
Python
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MIT License
•6•0•0•1•Updated Mar 20, 2024Mar 20, 2024
hum-varfish-annotator-fork
Public
Annotate variants for import into VarFish server.
Java
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MIT License
•3•0•0•0•Updated Dec 1, 2023Dec 1, 2023
hum-varfish-docker-compose-fork
Public
Setup VarFish as using Docker Compose
Makefile
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MIT License
•3•0•0•0•Updated Dec 1, 2023Dec 1, 2023
hum-varfish-server-fork
Public
VarFish: comprehensive DNA variant analysis for diagnostics and research
Python
•
MIT License
•11•0•0•0•Updated Dec 1, 2023Dec 1, 2023
hum-varfish-db-downloader-fork
Public
Download public/static databases for VarFish
Python
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MIT License
•3•0•0•0•Updated Dec 1, 2023Dec 1, 2023
hum-varfish-cli-fork
Public
VarFish REST API client (CLI + Python package)
Python
•
MIT License
•3•0•0•0•Updated Dec 1, 2023Dec 1, 2023
MultiQC
Public
Aggregate results from bioinformatics analyses across many samples into a single report.
Python
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GNU General Public License v3.0
•604•1•1•0•Updated Oct 26, 2023Oct 26, 2023
hum-gene-ranking-shootout
Public
A small benchmark for comparing gene ranking methods
Python
•
MIT License
•1•0•0•0•Updated May 11, 2023May 11, 2023
bioconda-recipes
Public
Conda recipes for the bioconda channel.
Shell
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MIT License
•3.3k•0•0•0•Updated Apr 5, 2023Apr 5, 2023
MultiQC_TestData
Public
Test data for MultiQC. See https://github.com/ewels/MultiQC
HTML
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MIT License
•145•0•0•0•Updated Mar 15, 2023Mar 15, 2023
scramble
Public
R
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Other
•12•0•0•0•Updated Apr 5, 2022Apr 5, 2022
LB-ncov2019-artic-nf
Public
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
Nextflow
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GNU Affero General Public License v3.0
•86•1•0•0•Updated Mar 14, 2022Mar 14, 2022
TBProfiler
Public
Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
Python
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GNU General Public License v3.0
•43•0•0•0•Updated Nov 24, 2021Nov 24, 2021