bihealth/tranter_vaccination_ASCT

This repository has been archived on 22/Mar/2024
Stars
1
Language
R
Created 10 months ago
Updated 10 months ago

bihealth/tranter_vaccination_ASCT

bihealth

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

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"

vcfpy

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

varfish-server

VarFish: comprehensive DNA variant analysis for diagnostics and research

NeatMS

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

scelvis

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

bih-cluster

BIH Cluster Wiki

digestiflow-server

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

sodar-core-legacy

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

sodar-server

SODAR: System for Omics Data Access and Retrieval

mehari

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

hlama

Simple matching of HTS samples based on HLA typing

metaquac

Metabolomics Targeted Quality Control

sodar-core

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

cnvetti

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

reev

REEV: Explanation and Evaluation of Variants

snappy-pipeline

SNAPPY Nucleic Acid Processing in Python

flowcelltool

Simple management of Illumina sequencing flowcells

hgvs-rs

A port of biocommons/hgvs to the Rust programming language

clinvar-tsv

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

clear-cnv

ClearCNV - CNV analysis in the presence of ambiguity and noise

auto-acmg

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

annonars

Genome annotation based on Rust and RocksDB

varfish-annotator

Annotate variants for import into VarFish server.

varfish-docker-compose

Setup VarFish as using Docker Compose

WiPP

large scale GC-MS data preprocessing workflow

altamisa

AltamISA: a Python API for ISA-Tab files

gene-ranking-shootout

A small benchmark for comparing gene ranking methods

cubi-tk

CUBI Tooling for SODAR, VarFish et al.

clinvar-this

ClinVar Submission API Made Easy

cubi_demux

Demultiplexing utility, companion to flowcelltool.

seqrepo-rs

A port of biocommons/seqrepo to the Rust programming language

varfish-db-downloader

Download public databases for VarFish

ngs-chew

Tasty, tasty, NGS!

snakemake-variant-enrichment

A Snakemake workflow for germline variant burden analyses.

RCrashCourse2023

clinvar_report

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

biomedsheets

📚 JSON/TSV sample sheets for biomedical experiments

spliceai-wrapper

Wrapper for Illumina SpliceAI that caches results

RcrashCourse2021

R Crash Course 2021

rodeos-ingest

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

sodar-docker-compose

Setup SODAR using Docker Compose

excovis

Exome Coverage Visualization

varfish-server-worker

Rust-based background worker for varfish-server

digestiflow-demux

🍝 Digestiflow Demultiplexing Tool

SigsPack

SigsPack R/Bioconductor package for mutational signature estimation

varfish-cli

VarFish REST API client (CLI + Python package)

cubi-isa-templates

CUBI ISA-Tab templates

Wei_et_al_2024

Jupyter Notebook

ood-bih-rstudio-server

Open OnDemand App: RStudio Server

annonars-data-clinvar

Clinvar data builds for annonars

varfish-wf-queries

VarFish (Snakemake) Client Workflow for Querying Snakemake

bioshmods

Shiny modules for bioinformatics

var-agg

Aggregate multi-sample VCF files "site VCF" files

seasnap-pipeline

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

bamspiker

Spike variants into BAM files (without all the hassle)

varfish-installer

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

kiosc-server

rodeos-docker-compose

Setup RODEOS ingest with docker compose

cadd-rest-api

Simple REST API wrapper for CADD-scripts.

sodar-django-site

Django site template for SODAR Core based projects

obermayer_et_al_tcell_persistence

hoffmann_et_al_bronchioalveolar_organoids

hoenzke_et_al_human_lungs_covid_ace2

summarize-cohort-vcf

Compute summaries for cohort VCF files

digestiflow-cli

🍝 Digestiflow Command Line Client

varfish-anno

DEPRECATED Convert annotation database files to Var🐟 import format

SC-RNA-Seq-37vs4

panelapp-pydantic

Pydanic models for GenomicsEngland PanelApp API

irods-docker

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

clinvar-data-jsonl

Weekly ClinVar releases as JSONL with additonal useful files

mehari-data-tx

Transcript data builds for mehari

sodar-cli

SODAR REST API client (CLI + Python package)