Computational Biology Group (CBG)

All

116 repositories

sr2silo
Public
Wrangling short-read sequencing data for import into SILO
Python
•
MIT License
•1•1•5•3•Updated Mar 16, 2026Mar 16, 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
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•27•2•Updated Mar 13, 2026Mar 13, 2026
pangolin
Public
BSSE COVID-19 sequencing of test swab samples
Shell
•3•7•0•1•Updated Mar 13, 2026Mar 13, 2026
CTC-SCITE
Public
Computational method and analyses to study the clonality of circulating tumor cell clusters
C++
•
GNU General Public License v3.0
•1•5•2•0•Updated Mar 12, 2026Mar 12, 2026
scClone2DR
Public
scClone2DR project
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Mar 12, 2026Mar 12, 2026
scDEF
Public
Deep exponential families for single-cell data.
matrix-factorization scrna-seq variational-inference
matrix-factorization scrna-seq variational-inference hierarchical-models single-cell-rna-seq jax batch-integration gene-signatures
Python
•1•20•0•0•Updated Mar 10, 2026Mar 10, 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•3•Updated Mar 8, 2026Mar 8, 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 Feb 27, 2026Feb 27, 2026
SC-Bulk-Domain-Adaptation
Public
Python
•
MIT License
•0•1•0•0•Updated Feb 26, 2026Feb 26, 2026
RSV-wastewater-V-pipe
Public
Wastewater-derived Respiratory Syncytial Virus data analysis
Python
•
Apache License 2.0
•0•0•0•0•Updated Feb 11, 2026Feb 11, 2026
v-pipe-scout
Public
Rapid Viral Variant Exploration and Detection - Interactive WebApp
biohackeu24 elixir-cloud-aai
biohackeu24 elixir-cloud-aai
Python
•
MIT License
•0•0•7•1•Updated Feb 1, 2026Feb 1, 2026
SCITE-RNA
Public
Jupyter Notebook
•
GNU General Public License v3.0
•1•5•1•0•Updated Jan 28, 2026Jan 28, 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
LolliPop
Public
Deconvolution for Wastewater Genomics
Jupyter Notebook
•
GNU General Public License v3.0
•0•7•7•6•Updated Jan 19, 2026Jan 19, 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•4•Updated Jan 5, 2026Jan 5, 2026
cojac
Public
Jupyter Notebook
•
GNU General Public License v3.0
•5•19•15•4•Updated Nov 24, 2025Nov 24, 2025
PYggdrasil
Public
Inference and analysis of mutation trees in Python
Python
•
MIT License
•0•6•5•1•Updated Nov 22, 2025Nov 22, 2025
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•144•39•3•Updated Nov 19, 2025Nov 19, 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 Oct 30, 2025Oct 30, 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 Oct 30, 2025Oct 30, 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 Oct 30, 2025Oct 30, 2025
mt-SCITE
Public
Tree inference from mitochondrial mutations
Jupyter Notebook
•1•5•1•0•Updated Oct 23, 2025Oct 23, 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•23•8•0•Updated Oct 21, 2025Oct 21, 2025
DCV-CrPV-cGAS-STING-pathway-data-analysis
Public
Jupyter Notebook
•0•1•0•0•Updated Oct 11, 2025Oct 11, 2025
HEV_sequencing_data_analysis
Public
Analysis of Illumina sequeincing data of Hepatitis E virus patient samples.
Jupyter Notebook
•0•0•0•0•Updated Oct 8, 2025Oct 8, 2025
bmi
Public
Mutual information estimators and benchmark
python benchmark estimator
python benchmark estimator mutual-information
Python
•
MIT License
•7•56•8•4•Updated Sep 16, 2025Sep 16, 2025
COMPASS
Public
C++
•
GNU General Public License v3.0
•11•25•7•0•Updated Aug 24, 2025Aug 24, 2025
oncotree2vec
Public
A method for embedding and clustering of tumor mutation trees.
Python
•0•8•0•0•Updated Aug 9, 2025Aug 9, 2025