bihealth/sodar-server

SODAR: System for Omics Data Access and Retrieval

Language: Python - Size: 15.8 MB - Last synced: about 19 hours ago - Pushed: about 19 hours ago - Stars: 13 - Forks: 3

bihealth/dotty

cdot-based transcript projections

Language: Python - Size: 290 KB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 0 - Forks: 0

bihealth/reev-docker-compose

REEV Docker Compose

Language: Shell - Size: 105 KB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 1

bihealth/reev-frontend-lib

Re-useable components from REEV

Language: TypeScript - Size: 3.88 MB - Last synced: 2 days ago - Pushed: 2 days ago - Stars: 0 - Forks: 1

bihealth/StemCNV-check

Language: Python - Size: 324 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

bihealth/ood-bih-matlab

Open OnDemand App: MATLAB

Language: HTML - Size: 73.2 KB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

bihealth/cubi-literature

CUBI publications

Language: HTML - Size: 7.33 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

bihealth/seasnap-pipeline

SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline

Language: Python - Size: 1.54 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 1 - Forks: 2

bihealth/vcfpy

Python 3 library with good support for both reading and writing VCF

Language: Python - Size: 1.25 MB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 87 - Forks: 18

bihealth/nf-core-configs Fork of nf-core/configs

Config files used to define parameters specific to compute environments at different Institutions

Language: Nextflow - Size: 46.3 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 0 - Forks: 0

bihealth/Wei_et_al_2024

Language: Jupyter Notebook - Size: 8.55 MB - Last synced: 22 days ago - Pushed: 22 days ago - Stars: 1 - Forks: 0

bihealth/bih-cluster

BIH Cluster Wiki

Language: Awk - Size: 27.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 13 - Forks: 36

bihealth/cubi-tk

CUBI Tooling for SODAR, VarFish et al.

Language: Python - Size: 917 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 4 - Forks: 6

bihealth/ngs-chew

Tasty, tasty, NGS!

Language: Python - Size: 149 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 1

bihealth/scelvis

:sparkler: SCelVis - web-based visualization of single-cell data. :arrow_right: :arrow_right: Demo :arrow_right::arrow_right:

Language: Python - Size: 70.8 MB - Last synced: 29 days ago - Pushed: 3 months ago - Stars: 21 - Forks: 5

bihealth/auto-acmg

A tool for automatic classification of sequence variants according to ACMG criteria.

Language: Python - Size: 479 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

bihealth/reev

REEV: Explanation and Evaluation of Variants

Language: TypeScript - Size: 8.77 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 4 - Forks: 1

bihealth/hpc-access

Web interface for managing access and resource requests for the BIH cluster

Language: Python - Size: 2.57 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

bihealth/snappy-pipeline

SNAPPY Nucleic Acid Processing in Python

Language: Python - Size: 7.57 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 4

bihealth/sodar-core

SODAR Core: A Django-based framework for building scientific data management web apps

Language: Python - Size: 7.23 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 8 - Forks: 1

bihealth/CCISM

Single Cell Identification of Tumor Cells by Expectation Maximization

Language: Python - Size: 78.1 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

bihealth/WiPP

large scale GC-MS data preprocessing workflow

Language: Python - Size: 348 MB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 5 - Forks: 3

bihealth/sodar-django-site

Django site template for SODAR Core based projects

Language: Python - Size: 291 KB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 1 - Forks: 0

bihealth/seasnap-pipeline-browser

Docker image build instructions for the sea-snap pipeline browser

Language: R - Size: 4.56 MB - Last synced: about 2 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

bihealth/seaPiper

Workflow output explorer for sea-snap

Language: R - Size: 2.9 MB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

bihealth/ood-bih-jupyter

Open OnDemand App: Jupyter

Language: HTML - Size: 27.3 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

bihealth/january-presentation-bioshmods

Language: HTML - Size: 4.55 MB - Last synced: about 2 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

bihealth/isaeditor

Tools for editing ISA-Tabs in R

Language: R - Size: 70.3 KB - Last synced: about 2 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

bihealth/exomiser-rest-api-mock

Mocking the Exomiser REST API for VarFish development.

Language: Python - Size: 1.95 KB - Last synced: about 2 months ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

bihealth/edu-hpc-crash-course

HPC Crash Course Slides

Language: JavaScript - Size: 31.2 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

bihealth/digestiflow-server

:cocktail: Web-based database system for flow cell management (incl. REST API)

Language: Python - Size: 3.26 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 15 - Forks: 2

bihealth/cada-prio-data

Weekly cada-prio model releases

Language: HCL - Size: 17.6 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

bihealth/manuscript-Microenvironmental-acidification

Language: HTML - Size: 2.77 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

bihealth/tranter_vaccination_ASCT 📦

code repository for Tranter et al. "Comparable CD8+ T cell responses to SARS-CoV-2 vaccination in single-cell transcriptomics of recently allogeneic transplanted patients and healthy individuals"

Language: R - Size: 22.5 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

bihealth/NeatMS 📦

NeatMS is an open source python package for untargeted LCMS signal labelling and filtering.

Language: Python - Size: 44.7 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 26 - Forks: 2

bihealth/metaquac 📦

Metabolomics Targeted Quality Control

Language: R - Size: 1.96 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 8 - Forks: 1

bihealth/altamisa

AltamISA: a Python API for ISA-Tab files

Language: Python - Size: 989 KB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 5 - Forks: 2

bihealth/biomedsheets

:books: JSON/TSV sample sheets for biomedical experiments

Language: Python - Size: 403 KB - Last synced: 4 days ago - Pushed: 3 months ago - Stars: 3 - Forks: 3

bihealth/kolla-ansible Fork of openstack/kolla-ansible

Ansible deployment of the Kolla containers. Mirror of code maintained at opendev.org.

Language: Jinja - Size: 23.4 MB - Last synced: about 2 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

bihealth/edu-bsc-beacon-julia

Repository for Bachelor Thesis for Julia (Beacons)

Language: Python - Size: 5.95 MB - Last synced: about 2 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

bihealth/hlama

Simple matching of HTS samples based on HLA typing

Language: Python - Size: 1.85 MB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 13 - Forks: 2

bihealth/snappy-use-case-germline 📦

SNAPPY use case "germline": from FASTQ to VarFish export

Language: Shell - Size: 26.4 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 1

bihealth/rodeos-docker-compose 📦

Setup RODEOS ingest with docker compose

Language: Makefile - Size: 9.77 KB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

bihealth/atlatl 📦

atlatl is a toolkit for targeted long read based genotyping and structural variation detection at candidate loci

Language: Python - Size: 2.3 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

bihealth/clear-cnv-supplementary 📦

supplementary material for the publication of clearCNV

Language: Python - Size: 3.49 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

bihealth/action-require-trailers 📦

GitHub Action to require commit message trailers

Language: JavaScript - Size: 1.59 MB - Last synced: about 2 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

bihealth/kayobe Fork of openstack/kayobe 📦

Deployment of containerised OpenStack to bare metal using kolla and bifrost. Mirror of code maintained at opendev.org.

Size: 4.3 MB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

bihealth/hoenzke_et_al_human_lungs_covid_ace2 📦

Language: Python - Size: 2.51 MB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

bihealth/hoffmann_et_al_bronchioalveolar_organoids 📦

Language: Python - Size: 23.4 KB - Last synced: about 2 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

bihealth/obermayer_et_al_tcell_persistence 📦

Language: R - Size: 31.3 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

bihealth/panelapp-pydantic

Pydanic models for GenomicsEngland PanelApp API

Language: Python - Size: 44.9 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

bihealth/django-plugins Fork of krischer/django-plugins

A Simple Plugin Framework for Django (maintained by @bihealth)

Language: Python - Size: 147 KB - Last synced: 13 days ago - Pushed: 5 months ago - Stars: 0 - Forks: 0

bihealth/MultiQC Fork of MultiQC/MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Language: Python - Size: 17 MB - Last synced: about 2 months ago - Pushed: almost 8 years ago - Stars: 0 - Forks: 0

bihealth/clingen-svi-comp_calibration Fork of vpejaver/clingen-svi-comp_calibration

Data and code associated with ClinGen-SVI computational sub-group's calibration paper

Size: 37.1 KB - Last synced: about 2 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

bihealth/SC-RNA-Seq-37vs4

Language: R - Size: 78.5 MB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

bihealth/sodar-cli

SODAR REST API client (CLI + Python package)

Language: Python - Size: 78.1 KB - Last synced: about 1 month ago - Pushed: 4 months ago - Stars: 1 - Forks: 1

bihealth/irods-docker

Docker container that runs an iRODS server (iCAT enabled or not).

Language: Jinja - Size: 37.1 KB - Last synced: about 2 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

bihealth/sodar-docker-compose

Setup SODAR using Docker Compose

Language: Shell - Size: 59.6 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 2

bihealth/cubi-isa-templates

CUBI ISA-Tab templates

Language: Python - Size: 107 KB - Last synced: about 20 hours ago - Pushed: about 21 hours ago - Stars: 2 - Forks: 3

bihealth/edu-hpc-biomedical-research

Course: High Performance Compute in Biomedical Research

Language: JavaScript - Size: 33.3 MB - Last synced: about 2 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

bihealth/cookiecutter-python-cubi 📦

A cookiecutter with useful boilerplate

Language: Python - Size: 32.2 KB - Last synced: about 2 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

bihealth/spliceai-wrapper 📦

Wrapper for Illumina SpliceAI that caches results

Language: Python - Size: 43 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

bihealth/ood-bih-rstudio-server

Open OnDemand App: RStudio Server

Language: Shell - Size: 37.1 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 1 - Forks: 0

bihealth/ngs_glutton 📦

Python library for reading raw sequencing output.

Language: Python - Size: 55.7 KB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

bihealth/var-agg 📦

Aggregate multi-sample VCF files "site VCF" files

Language: Rust - Size: 28.3 KB - Last synced: about 2 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

bihealth/summarize-cohort-vcf 📦

Compute summaries for cohort VCF files

Language: Java - Size: 8.79 KB - Last synced: about 2 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

bihealth/flowcelltool 📦

Simple management of Illumina sequencing flowcells

Language: Python - Size: 1.22 MB - Last synced: about 2 months ago - Pushed: over 5 years ago - Stars: 7 - Forks: 1

bihealth/cbioportal_users 📦

A quick hack for user management in cBioPortal developed by CUBI/BIH.

Language: Python - Size: 21.5 KB - Last synced: about 2 months ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

bihealth/RCrashCourse2023

Language: HTML - Size: 80.6 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 2 - Forks: 0

bihealth/varfish-wf-validation

VarFish (Snakemake) Client Workflow for Querying Snakemake

Language: Python - Size: 12.7 KB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

bihealth/varfish-course-scripts

Scripts for generating the data used in the VarFish course

Language: Python - Size: 233 KB - Last synced: 10 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

bihealth/varfish-installer

DEPRECATED, use https://github.com/bihealth/varfish-docker-compose instead

Language: Makefile - Size: 60.5 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

bihealth/varfish-clinical-beacon-client

Language: Python - Size: 5.86 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

bihealth/varfish-anno

DEPRECATED Convert annotation database files to Var:fish: import format

Language: Makefile - Size: 18.6 KB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

bihealth/sodar-docker-env 📦

SODAR developement and testing environment

Language: Shell - Size: 17.6 KB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

bihealth/snappy-use-case-cancer

SNAPPY use case "cancer": from FASTQ to cBioPortal export

Size: 1.95 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

bihealth/singularity-matlab

Singularity image for Matlab

Size: 0 Bytes - Last synced: 10 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

bihealth/kiosc-example-seapiper

Size: 0 Bytes - Last synced: 10 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

bihealth/file-exchange-worker

File Exchange Worker

Size: 0 Bytes - Last synced: 10 months ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

bihealth/edu-hpc-labs

HPC Labs Code

Size: 0 Bytes - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

bihealth/cookiecutter-isatab-germline

Cookiecutter template for ISA-Tab germline DNA sequencing (exome/genome)

Size: 12.7 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

bihealth/cookiecutter-isatab-generic

Cookiecutter template for ISA-Tab germline DNA sequencing (generic/functional studies)

Size: 5.86 KB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

bihealth/cookiecutter-ansible-role

Cookiecutter template CUBI Ansible roles

Language: Python - Size: 11.7 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

bihealth/cbioportal Fork of cBioPortal/cbioportal

Fork of bioportal for our changes.

Language: JavaScript - Size: 197 MB - Last synced: 10 months ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-varfish-server

Ansible role bihealth.varfish_server

Language: Shell - Size: 24.4 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

bihealth/ansible-role-sssd

Ansible role bihealth.sssd

Language: Python - Size: 6.84 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-ssl-certs

Ansible role bihealth.ssl_certs

Language: HTML - Size: 13.7 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-ssh-keys

Ansible role bihealth.ssh_keys

Language: Python - Size: 12.7 KB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-sodar-taskflow

Ansible role bihealth.sodar_taskflow (source and CI internal for now).

Language: Python - Size: 8.79 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-sodar-server

Ansible role bihealth.sodar_server (source and CI internal for now).

Language: HTML - Size: 20.5 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-sodar-core-app

Ansible role bihealth.sodar_core_app

Language: HTML - Size: 34.2 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-redis

Ansible role bihealth.redis

Language: HTML - Size: 23.4 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-provision-proxmox

Ansible role bihealth.provision-proxmox

Size: 121 KB - Last synced: 10 months ago - Pushed: about 3 years ago - Stars: 2 - Forks: 1

bihealth/ansible-role-python3

Ansible role bihealth.python3

Language: Python - Size: 7.81 KB - Last synced: 10 months ago - Pushed: about 4 years ago - Stars: 2 - Forks: 1

bihealth/ansible-role-postgres-server

Ansible role bihealth.postgres_server

Language: HTML - Size: 29.3 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 3

bihealth/ansible-role-nginx

Ansible role bihealth.nginx

Language: Python - Size: 12.7 KB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-memcached

Ansible role bihealth.memcached

Language: Python - Size: 5.86 KB - Last synced: 10 months ago - Pushed: almost 5 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-postgres-client

Ansible role bihealth.postgres_client

Language: Python - Size: 11.7 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

bihealth/ansible-role-jannovar-server

Ansible role bihealth.jannovar_server

Language: HTML - Size: 12.7 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

bihealth/ansible-role-minio-server

Ansible role bihealth.minio_server

Language: Python - Size: 6.84 KB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0