Computational Biology Group (CBG)

All

104 repositories

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•133•31•5•Updated Dec 23, 2024Dec 23, 2024
SCICoNE
Public
Single-cell copy number calling and event history reconstruction.
cancer-genomics bayesian-inference mcmc single-cell copy-number-variation
C++
•
GNU General Public License v3.0
•7•20•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
•
MIT License
•0•3•1•0•Updated Dec 20, 2024Dec 20, 2024
sr2silo
Public
Wrangling short-read sequencing data for import into SILO
Python
•
MIT License
•0•1•5•2•Updated Dec 20, 2024Dec 20, 2024
LolliPop
Public
Deconvolution for Wastewater Genomics
Jupyter Notebook
•
GNU General Public License v3.0
•1•4•3•1•Updated Dec 19, 2024Dec 19, 2024
vpipe-biohack24-frontend
Public
Cloudification of V-Pipe: Frontend for the Biohackathon 2024
biohackeu24 elixir-cloud-aai
Python
•
MIT License
•0•0•0•0•Updated Dec 17, 2024Dec 17, 2024
pangolin
Public
BSSE COVID-19 sequencing of test swab samples
Shell
•3•7•1•2•Updated Dec 13, 2024Dec 13, 2024
GSoD-2024
Public
Google Season of Docs 2024
0•1•0•0•Updated Dec 10, 2024Dec 10, 2024
CTC-SCITE
Public
Computational method and analyses to study the clonality of circulating tumor cell clusters
C++
•
GNU General Public License v3.0
•1•2•3•0•Updated Dec 10, 2024Dec 10, 2024
bmi
Public
Mutual information estimators and benchmark
python benchmark estimator mutual-information
Python
•
MIT License
•6•39•9•2•Updated Dec 5, 2024Dec 5, 2024
VILOCA
Public
VILOCA: VIral LOcal haplotype reconstruction and mutation CAlling for short and long read data
Python
•
GNU General Public License v3.0
•0•14•1•0•Updated Dec 3, 2024Dec 3, 2024
oncotreeVIS
Public
An interactive graphical user interface for visualizing mutation tree cohorts.
JavaScript
•
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
•
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
•
GNU General Public License v3.0
•0•1•0•0•Updated Nov 30, 2024Nov 30, 2024
covvfit
Public
Fitness estimates of SARS-CoV-2 variants
epidemiology bayesian-statistics fitness-landscape sars-cov-2
Python
•
MIT License
•0•0•5•3•Updated Nov 28, 2024Nov 28, 2024
cojac
Public
Jupyter Notebook
•
GNU General Public License v3.0
•5•19•13•0•Updated Nov 27, 2024Nov 27, 2024
mt-SCITE
Public
Tree inference from mitochondrial mutations
Jupyter Notebook
•1•4•0•0•Updated Nov 24, 2024Nov 24, 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
•
Other
•0•2•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•5•0•0•Updated Nov 8, 2024Nov 8, 2024
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 Nov 7, 2024Nov 7, 2024
SCITE-RNA
Public
Jupyter Notebook
•0•0•0•0•Updated Nov 5, 2024Nov 5, 2024
mnem
Public
Mixture Nested Effects Models - https://doi.org/10.1093/bioinformatics/bty602 - https://bioconductor.org/packages/mnem
R
•3•4•0•0•Updated Nov 4, 2024Nov 4, 2024
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 Nov 4, 2024Nov 4, 2024
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 Nov 4, 2024Nov 4, 2024
mixmax
Public
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
UsefulGnom
Public
Useful Genomic Tools
Python
•0•0•1•1•Updated Oct 25, 2024Oct 25, 2024
SARS-CoV-2-wastewater-sample-processing-VILOCA
Public
wastewater-sample-processing-VILOCA
Jupyter Notebook
•
Apache License 2.0
•1•2•0•0•Updated Oct 22, 2024Oct 22, 2024
viloca_applications
Public
This repo contains applications of the tool VILOCA.
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Oct 17, 2024Oct 17, 2024