Computational Biology Group (CBG)

All

111 repositories

sr2silo
Public
Wrangling short-read sequencing data for import into SILO
Python
•
MIT License
•1•1•15•3•Updated Jul 7, 2025Jul 7, 2025
cowwid
Public
Procedure used fro the surveillance of SARS-CoV-2 genomic variants in wastewater.
covid-19 sars-cov-2 bioinformatics pipeline ngs
Jupyter Notebook
•
Other
•1•7•0•1•Updated Jul 3, 2025Jul 3, 2025
WisePulse
Public
WISE Loculus with V-Pipe – Infra for start-to-end viral wastewater analysis.
Rust
•
MIT License
•0•1•3•1•Updated Jul 2, 2025Jul 2, 2025
V-pipe
Public
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
snakemake virus sequencing conda bioinformatics-pipeline hiv sars-cov-2 sarscov2 biohackeu20 biohackcovid20
Jupyter Notebook
•
Apache License 2.0
•46•138•34•6•Updated Jul 1, 2025Jul 1, 2025
VILOCA
Public
VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
Python
•
GNU General Public License v3.0
•1•21•7•0•Updated Jul 1, 2025Jul 1, 2025
pangolin
Public
BSSE COVID-19 sequencing of test swab samples
Shell
•3•7•0•0•Updated Jul 1, 2025Jul 1, 2025
covvfit
Public
Fitness estimates of SARS-CoV-2 variants
epidemiology forecasting-models fitness-landscape virology statistical-modeling sars-cov-2 wastewater-surveillance wastewater-based-epidemiology
Python
•
MIT License
•0•2•4•4•Updated Jul 1, 2025Jul 1, 2025
PYggdrasil
Public
Inference and analysis of mutation trees in Python
Python
•
MIT License
•0•6•4•0•Updated Jun 26, 2025Jun 26, 2025
oncotree2vec
Public
A method for embedding and clustering of tumor mutation trees.
Python
•0•8•0•0•Updated Jun 21, 2025Jun 21, 2025
v-pipe-scout
Public
Rapid Viral Variant Exploration and Detection - Interactive WebApp
biohackeu24 elixir-cloud-aai
Python
•
MIT License
•1•0•10•0•Updated Jun 4, 2025Jun 4, 2025
smallgenomeutilities
Public
smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.
Python
•
GNU General Public License v2.0
•8•11•2•0•Updated May 27, 2025May 27, 2025
CTC-SCITE
Public
Computational method and analyses to study the clonality of circulating tumor cell clusters
C++
•
GNU General Public License v3.0
•1•4•2•0•Updated May 27, 2025May 27, 2025
LongSom
Public
LongSom tool for long-reads
Python
•1•10•3•1•Updated May 20, 2025May 20, 2025
mnem
Public
Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem
R
•3•4•0•0•Updated May 20, 2025May 20, 2025
cojac
Public
Jupyter Notebook
•
GNU General Public License v3.0
•5•19•13•0•Updated May 17, 2025May 17, 2025
LolliPop
Public
Deconvolution for Wastewater Genomics
Jupyter Notebook
•
GNU General Public License v3.0
•1•3•3•0•Updated May 16, 2025May 16, 2025
pMHN
Public
Personalised mutual hazard networks: fixed effects in cancer progression modeling
probabilistic-models cancer-evolution
Python
•
MIT License
•0•3•1•0•Updated May 9, 2025May 9, 2025
Jnotype
Public
Probabilistic modeling of high-dimensional binary data in JAX
clustering cancer-genomics unsupervised-learning bayesian-statistics jax probabilistic-machine-learning ideal-point-estimation
Python
•
Other
•0•3•6•3•Updated May 9, 2025May 9, 2025
GenoRepro
Public
Reproducibility Project
Python
•0•0•0•0•Updated May 7, 2025May 7, 2025
oncotreeVIS
Public
An interactive graphical user interface for visualizing mutation tree cohorts.
JavaScript
•
MIT License
•0•0•0•0•Updated May 3, 2025May 3, 2025
RSV-wastewater-V-pipe
Public
Wastewater-derived Respiratory Syncytial Virus data analysis
Python
•
Apache License 2.0
•0•0•0•0•Updated May 2, 2025May 2, 2025
Influenza_wastewater_analysis
Public
R
•0•0•1•0•Updated Apr 25, 2025Apr 25, 2025
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 22, 2025Apr 22, 2025
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 22, 2025Apr 22, 2025
tupro-evolutionary-landscapes
Public
Python
•0•0•0•0•Updated Apr 15, 2025Apr 15, 2025
mt-SCITE
Public
Tree inference from mitochondrial mutations
Jupyter Notebook
•1•5•0•0•Updated Apr 4, 2025Apr 4, 2025
FiTree
Public
FiTree: Bayesian inference of fitness landscapes via tree-structured branching processes
Jupyter Notebook
•
MIT License
•0•4•0•0•Updated Mar 28, 2025Mar 28, 2025
DCV-CrPV-cGAS-STING-pathway-data-analysis
Public
Jupyter Notebook
•0•1•0•0•Updated Mar 26, 2025Mar 26, 2025
conda_stats_gather
Public
Used to track downloads of bioconda packages used by V-pipe, see: https://cbg-ethz.github.io/V-pipe/pipeline/
Perl
•0•0•0•0•Updated Mar 5, 2025Mar 5, 2025
fairClust
Public
R
•
MIT License
•0•1•0•0•Updated Mar 5, 2025Mar 5, 2025