Discover bihealth/bioshmods Open Source project

VarFish: comprehensive DNA variant analysis for diagnostics and research

varfish-server

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

NeatMS

🎇 SCelVis - web-based visualization of single-cell data. ➡️ ➡️ Demo ➡️➡️

scelvis

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

bih-cluster

BIH Cluster Wiki

Awk

digestiflow-server

LEGACY repository for SODAR Core, preserved for saving review-related issues. See "sodar-core" for the up-to-date repository.

sodar-core-legacy

SODAR: System for Omics Data Access and Retrieval

sodar-server

VEP-like tool for sequence ontology and HGVS annotation of VCF files

mehari

Simple matching of HTS samples based on HLA typing

hlama

Metabolomics Targeted Quality Control

metaquac

sodar-core

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

🎉 CNVetti – robust, efficient, and versatile clinical CNV calling from HTS data

cnvetti

REEV: Explanation and Evaluation of Variants

reev

TypeScript

snappy-pipeline

SNAPPY Nucleic Acid Processing in Python

Simple management of Illumina sequencing flowcells

flowcelltool

A port of biocommons/hgvs to the Rust programming language

hgvs-rs

Pipeline for converting ClinVar XML files to easy-to-use TSV files

clinvar-tsv

ClearCNV - CNV analysis in the presence of ambiguity and noise

clear-cnv

Automatic classification of sequence variants and CNVs according to ACMG criteria.

auto-acmg

Genome annotation based on Rust and RocksDB

annonars

Annotate variants for import into VarFish server.

varfish-annotator

Java

varfish-docker-compose

Setup VarFish as using Docker Compose

large scale GC-MS data preprocessing workflow

WiPP

AltamISA: a Python API for ISA-Tab files

altamisa

A small benchmark for comparing gene ranking methods

gene-ranking-shootout

CUBI Tooling for SODAR, VarFish et al.

cubi-tk

ClinVar Submission API Made Easy

clinvar-this

Demultiplexing utility, companion to flowcelltool.

cubi_demux

A port of biocommons/seqrepo to the Rust programming language

seqrepo-rs

Download public databases for VarFish

varfish-db-downloader

ngs-chew

Tasty, tasty, NGS!

A Snakemake workflow for germline variant burden analyses.

snakemake-variant-enrichment

Generate HTML reports from Clinvar-annotated VCF files (through Jannovar)

RCrashCourse2023

HTML

clinvar_report

📚 JSON/TSV sample sheets for biomedical experiments

biomedsheets

Wrapper for Illumina SpliceAI that caches results

spliceai-wrapper

Code for ingesting omics data into omics storage based on iRODS capabilities

RcrashCourse2021

R Crash Course 2021

HTML

rodeos-ingest

Setup SODAR using Docker Compose

sodar-docker-compose

Exome Coverage Visualization

excovis

Rust-based background worker for varfish-server

varfish-server-worker

🍝 Digestiflow Demultiplexing Tool

digestiflow-demux

SigsPack R/Bioconductor package for mutational signature estimation

SigsPack

varfish-cli

VarFish REST API client (CLI + Python package)

cubi-isa-templates

CUBI ISA-Tab templates

Open OnDemand App: RStudio Server

Wei_et_al_2024

Jupyter Notebook

ood-bih-rstudio-server

Clinvar data builds for annonars

annonars-data-clinvar

HCL

varfish-wf-queries

VarFish (Snakemake) Client Workflow for Querying Snakemake

Aggregate multi-sample VCF files "site VCF" files

var-agg

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

seasnap-pipeline

Spike variants into BAM files (without all the hassle)

bamspiker

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

varfish-installer

Makefile

kiosc-server

Setup RODEOS ingest with docker compose

rodeos-docker-compose

Makefile

cadd-rest-api

Simple REST API wrapper for CADD-scripts.

Django site template for SODAR Core based projects

sodar-django-site

obermayer_et_al_tcell_persistence

hoffmann_et_al_bronchioalveolar_organoids

hoenzke_et_al_human_lungs_covid_ace2

Compute summaries for cohort VCF files

summarize-cohort-vcf

Java

digestiflow-cli

🍝 Digestiflow Command Line Client

DEPRECATED Convert annotation database files to Var🐟 import format

varfish-anno

Makefile

SC-RNA-Seq-37vs4

panelapp-pydantic

Pydanic models for GenomicsEngland PanelApp API

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

irods-docker

Jinja

clinvar-data-jsonl

Weekly ClinVar releases as JSONL with additonal useful files

HCL

mehari-data-tx

Transcript data builds for mehari

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"

tranter_vaccination_ASCT

sodar-cli

SODAR REST API client (CLI + Python package)