cbg-ethz repositories

120 repositories

WisePulse
Public
WISE Loculus with V-Pipe – Infra for start-to-end viral wastewater analysis.
bioinformatics genomics public-health
bioinformatics genomics public-health wastewater-surveillance loculus viral-surveillance
Rust
•
MIT License
•0•5•36•2•Updated Oct 8, 2026Oct 8, 2026
sr2silo
Public
Wrangling short-read sequencing data for import into SILO
Python
•
MIT License
•2•1•8•9•Updated Oct 6, 2026Oct 6, 2026
RSV-wastewater-V-pipe
Public
Wastewater-derived Respiratory Syncytial Virus data analysis
Python
•
Apache License 2.0
•0•0•0•0•Updated Oct 5, 2026Oct 5, 2026
RSV-wastewater-2024-2025
Public
Computational analysis of wastewater-derived Respiratory Syncytial Virus (RSV) data collected during the 2024–2025 season in Switzerland.
Jupyter Notebook
•
Apache License 2.0
•0•0•0•0•Updated Oct 5, 2026Oct 5, 2026
cowwid
Public
Procedure used for the surveillance of SARS-CoV-2, RSV and Influenza genomic variants in wastewater.
bioinformatics pipeline ngs
bioinformatics pipeline ngs covid-19 sars-cov-2
Jupyter Notebook
•
Other
•0•7•3•3•Updated Oct 1, 2026Oct 1, 2026
pangolin
Public
BSSE COVID-19 sequencing of test swab samples
Shell
•3•7•0•1•Updated Oct 1, 2026Oct 1, 2026
SC-Bulk-Domain-Adaptation
Public
Python
•
MIT License
•0•2•0•0•Updated Sep 29, 2026Sep 29, 2026
scClone2DR
Public
scClone2DR project
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•1•0•0•Updated Sep 27, 2026Sep 27, 2026
MTBP_Numerics
Public
C++
•
MIT License
•0•0•0•0•Updated Sep 7, 2026Sep 7, 2026
scReliability_paper
Public
Python
•
MIT License
•0•5•0•0•Updated Sep 7, 2026Sep 7, 2026
SCICoNE
Public
Single-cell copy number calling and event history reconstruction.
cancer-genomics bayesian-inference mcmc
cancer-genomics bayesian-inference mcmc single-cell copy-number-variation
C++
•
GNU General Public License v3.0
•11•29•9•0•Updated Sep 3, 2026Sep 3, 2026
v-pipe-scout
Public
Rapid Viral Variant Exploration and Detection - Interactive WebApp
biohackeu24 elixir-cloud-aai
biohackeu24 elixir-cloud-aai
Python
•
MIT License
•1•0•7•7•Updated Aug 27, 2026Aug 27, 2026
scDEF
Public
Deep exponential families for single-cell data.
matrix-factorization scrna-seq trajectory-analysis
matrix-factorization scrna-seq trajectory-analysis variational-inference hierarchical-models single-cell-rna-seq jax batch-integration gene-signatures
Python
•1•21•0•2•Updated Aug 17, 2026Aug 17, 2026
mixmax
Public
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 11, 2026Aug 11, 2026
smallgenomeutilities
Public
smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.
Python
•
GNU General Public License v2.0
•7•10•3•6•Updated Aug 10, 2026Aug 10, 2026
V-pipe
Public
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
bioinformatics snakemake virus
bioinformatics snakemake virus genomics ngs sequencing conda bioinformatics-pipeline hiv sars-cov-2
Jupyter Notebook
•
Apache License 2.0
•46•147•39•2•Updated Aug 2, 2026Aug 2, 2026
demoTape
Public
Computational demultiplexing of targeted single-cell sequencing (tapestri) data
Python
•
GNU General Public License v3.0
•0•2•0•0•Updated Jul 24, 2026Jul 24, 2026
SCITE-RNA
Public
Jupyter Notebook
•
GNU General Public License v3.0
•1•6•1•0•Updated Jul 16, 2026Jul 16, 2026
mt-SCITE-benchmark
Public
Perform a benchmark comparing mt-scite to scite and merlin.
Python
•1•0•0•0•Updated Jul 14, 2026Jul 14, 2026
mt-SCITE
Public
Tree inference from mitochondrial mutations
Jupyter Notebook
•1•4•0•0•Updated Jun 19, 2026Jun 19, 2026
covvfit
Public
Fitness estimates of SARS-CoV-2 variants
epidemiology forecasting-models fitness-landscape
epidemiology forecasting-models fitness-landscape virology statistical-modeling sars-cov-2 wastewater-surveillance wastewater-based-epidemiology
Python
•
MIT License
•1•3•3•7•Updated Jun 1, 2026Jun 1, 2026
scReliability
Public
0•0•0•0•Updated May 8, 2026May 8, 2026
nempi
Public
Nested Effects Models based Perturbation Inference - https://doi.org/10.1093/bioinformatics/btab113 - https://bioconductor.org/packages/nempi
R
•1•2•0•0•Updated Apr 28, 2026Apr 28, 2026
mnem
Public
Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem
R
•3•4•0•0•Updated Apr 28, 2026Apr 28, 2026
epiNEM
Public
Epistatic Nested Effects Models - https://doi.org/10.1371/journal.pcbi.1005496 - https://bioconductor.org/packages/epiNEM/
R
•1•1•0•0•Updated Apr 28, 2026Apr 28, 2026
PYggdrasil
Public
Inference and analysis of mutation trees in Python
Python
•
MIT License
•0•6•5•1•Updated Apr 26, 2026Apr 26, 2026
Jnotype
Public
Probabilistic modeling of high-dimensional binary data in JAX
clustering cancer-genomics unsupervised-learning
clustering cancer-genomics unsupervised-learning bayesian-statistics jax probabilistic-machine-learning ideal-point-estimation
Python
•
Other
•0•3•6•2•Updated Mar 15, 2026Mar 15, 2026
pMHN
Public
Personalised mutual hazard networks: fixed effects in cancer progression modeling
probabilistic-models cancer-evolution
probabilistic-models cancer-evolution
Python
•
MIT License
•0•3•1•0•Updated Mar 14, 2026Mar 14, 2026
CTC-SCITE
Public
Computational method and analyses to study the clonality of circulating tumor cell clusters
C++
•
GNU General Public License v3.0
•2•5•3•0•Updated Mar 12, 2026Mar 12, 2026
hive-protocol
Public
The definitive protocol for Python in computational biology - workshop for CBG Retreat 2026
python research ci-cd
python research ci-cd bioinformatics-analysis
Python
•
MIT License
•3•5•0•0•Updated Jan 20, 2026Jan 20, 2026

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Computational Biology Group (CBG)

All

120 repositories

WisePulse

sr2silo

RSV-wastewater-V-pipe

RSV-wastewater-2024-2025

cowwid

pangolin

SC-Bulk-Domain-Adaptation

scClone2DR

MTBP_Numerics

scReliability_paper

SCICoNE

v-pipe-scout

scDEF

mixmax

smallgenomeutilities

V-pipe

demoTape

SCITE-RNA

mt-SCITE-benchmark

mt-SCITE

covvfit

scReliability

nempi

mnem

epiNEM

PYggdrasil

Jnotype

pMHN

CTC-SCITE

hive-protocol

Repositories list

120 repositories