Computational Biology Group (CBG)

All

107 repositories

VILOCA
Public
VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
Python
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GNU General Public License v3.0
•1•17•4•0•Updated Mar 6, 2025Mar 6, 2025
sr2silo
Public
Wrangling short-read sequencing data for import into SILO
Python
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MIT License
•0•1•16•2•Updated Mar 6, 2025Mar 6, 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
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
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Apache License 2.0
•47•135•34•5•Updated Mar 5, 2025Mar 5, 2025
RSV-wastewater-V-pipe
Public
Wastewater-derived Respiratory Syncytial Virus data analysis
Python
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Apache License 2.0
•0•0•0•0•Updated Mar 5, 2025Mar 5, 2025
fairClust
Public
R
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MIT License
•0•1•0•0•Updated Mar 5, 2025Mar 5, 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
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MIT License
•0•0•6•4•Updated Mar 4, 2025Mar 4, 2025
smallgenomeutilities
Public
smallgenomeutilities is a collection of Python scripts to convert alignments between different reference genomes.
Python
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GNU General Public License v2.0
•7•10•4•2•Updated Mar 3, 2025Mar 3, 2025
vpipe-biohack24-frontend
Public
Cloudification of V-Pipe: Frontend for the Biohackathon 2024
biohackeu24 elixir-cloud-aai
Python
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MIT License
•0•0•0•0•Updated Feb 28, 2025Feb 28, 2025
mt-SCITE-benchmark
Public
Perform a benchmark comparing mt-scite to scite and merlin.
Python
•0•0•0•0•Updated Feb 28, 2025Feb 28, 2025
mt-SCITE
Public
Tree inference from mitochondrial mutations
Jupyter Notebook
•1•4•0•0•Updated Feb 28, 2025Feb 28, 2025
pangolin
Public
BSSE COVID-19 sequencing of test swab samples
Shell
•3•7•2•2•Updated Feb 26, 2025Feb 26, 2025
CTC-SCITE
Public
Computational method and analyses to study the clonality of circulating tumor cell clusters
C++
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GNU General Public License v3.0
•1•2•3•0•Updated Feb 26, 2025Feb 26, 2025
LolliPop
Public
Deconvolution for Wastewater Genomics
Jupyter Notebook
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GNU General Public License v3.0
•1•3•2•0•Updated Feb 11, 2025Feb 11, 2025
lollipop-in-cloud
Public
On the fly variant deconvolution running in the cloud for on demand user requests.
biohackeu24 elixir-cloud-aai
Python
•0•0•0•0•Updated Feb 10, 2025Feb 10, 2025
FiTree
Public
FiTree: Bayesian inference of fitness landscapes via tree-structured branching processes
Python
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MIT License
•0•1•0•0•Updated Feb 6, 2025Feb 6, 2025
bmi
Public
Mutual information estimators and benchmark
python benchmark estimator mutual-information
Python
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MIT License
•6•44•8•2•Updated Jan 18, 2025Jan 18, 2025
LongSom
Public
LongSom tool for long-reads
Python
•0•8•2•0•Updated Jan 13, 2025Jan 13, 2025
demoTape
Public
Computational demultiplexing of targeted single-cell sequencing (tapestri) data
Python
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GNU General Public License v3.0
•0•2•0•0•Updated Jan 12, 2025Jan 12, 2025
SCICoNE
Public
Single-cell copy number calling and event history reconstruction.
cancer-genomics bayesian-inference mcmc single-cell copy-number-variation
C++
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GNU General Public License v3.0
•7•21•7•0•Updated Dec 21, 2024Dec 21, 2024
pMHN
Public
Personalised mutual hazard networks: fixed effects in cancer progression modeling
probabilistic-models cancer-evolution
Python
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MIT License
•0•3•1•0•Updated Dec 20, 2024Dec 20, 2024
GSoD-2024
Public
Google Season of Docs 2024
0•1•0•0•Updated Dec 10, 2024Dec 10, 2024
oncotreeVIS
Public
An interactive graphical user interface for visualizing mutation tree cohorts.
JavaScript
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MIT License
•0•0•0•0•Updated Dec 3, 2024Dec 3, 2024
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
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Other
•0•7•1•0•Updated Dec 2, 2024Dec 2, 2024
myeloid-clustering
Public
This repository contains supplementary information, data and code for the manuscript: Bayer et al. 2023, "Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies"
clustering cancer-genomics bayesian-networks myelodysplasticsyndome acute-myeloid-leukemia network-based-stratification
R
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GNU General Public License v3.0
•0•1•0•0•Updated Nov 30, 2024Nov 30, 2024
cojac
Public
Jupyter Notebook
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GNU General Public License v3.0
•5•19•13•0•Updated Nov 27, 2024Nov 27, 2024
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
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Other
•0•3•6•1•Updated Nov 18, 2024Nov 18, 2024
tupro-evolutionary-landscapes
Public
Python
•0•0•0•0•Updated Nov 15, 2024Nov 15, 2024
scDEF
Public
Deep exponential families for single-cell data.
matrix-factorization scrna-seq variational-inference hierarchical-models single-cell-rna-seq jax batch-integration gene-signatures
Python
•1•21•0•0•Updated Nov 13, 2024Nov 13, 2024
oncotree2vec
Public
A method for embedding and clustering of tumor mutation trees.
JavaScript
•0•7•0•0•Updated Nov 8, 2024Nov 8, 2024