Computational Biology Group (CBG)

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99 repositories

sr2silo
Public
Wrangling short-read sequencing data for import into SILO
Python
•
MIT License
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
mixmax
Public
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
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
•46•130•32•5•Updated Oct 31, 2024Oct 31, 2024
oncotreeVIS
Public
JavaScript
•0•0•0•0•Updated Oct 31, 2024Oct 31, 2024
pangolin
Public
BSSE COVID-19 sequencing of test swab samples
Shell
•3•7•1•2•Updated Oct 29, 2024Oct 29, 2024
oncotree2vec
Public
JavaScript
•0•3•0•0•Updated Oct 28, 2024Oct 28, 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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MIT License
•0•2•6•1•Updated Oct 27, 2024Oct 27, 2024
SCITE-RNA
Public
C++
•0•0•0•0•Updated Oct 25, 2024Oct 25, 2024
SARS-CoV-2-wastewater-sample-processing-VILOCA
Public
wastewater-sample-processing-VILOCA
Jupyter Notebook
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Apache License 2.0
•1•2•0•0•Updated Oct 22, 2024Oct 22, 2024
mt-SCITE
Public
Tree inference from mitochondrial mutations
Jupyter Notebook
•1•4•0•0•Updated Oct 21, 2024Oct 21, 2024
viloca_applications
Public
This repo contains applications of the tool VILOCA.
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Oct 17, 2024Oct 17, 2024
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
•0•14•0•0•Updated Oct 17, 2024Oct 17, 2024
ObservationMHN
Public
R
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MIT License
•0•2•0•0•Updated Oct 16, 2024Oct 16, 2024
LolliPop
Public
Deconvolution for Wastewater Genomics
Jupyter Notebook
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GNU General Public License v3.0
•1•4•0•2•Updated Oct 16, 2024Oct 16, 2024
pybda
Public
💻💻💻 A commandline tool for analysis of big biological data sets for distributed HPC clusters.
python machine-learning big-data apache-spark snakemake
Python
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GNU General Public License v3.0
•4•9•6•1•Updated Oct 15, 2024Oct 15, 2024
bmi
Public
Mutual information estimators and benchmark
python benchmark estimator mutual-information
Python
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MIT License
•5•35•8•2•Updated Oct 15, 2024Oct 15, 2024
LongSom
Public
LongSom tool for long-reads
Python
•0•5•2•0•Updated Oct 14, 2024Oct 14, 2024
cojac
Public
Jupyter Notebook
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GNU General Public License v3.0
•5•18•13•0•Updated Oct 11, 2024Oct 11, 2024
MARCS
Public
R
•0•0•0•0•Updated Sep 26, 2024Sep 26, 2024
COMPASS
Public
C++
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GNU General Public License v3.0
•10•19•5•0•Updated Sep 11, 2024Sep 11, 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 Sep 9, 2024Sep 9, 2024
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 Sep 3, 2024Sep 3, 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•20•0•0•Updated Sep 3, 2024Sep 3, 2024
SCATrEx
Public
Map single-cell transcriptomes to copy number evolutionary trees.
cancer-genomics scrna-seq copy-number-variation jax
Python
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Other
•1•13•3•0•Updated Aug 18, 2024Aug 18, 2024
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 Aug 14, 2024Aug 14, 2024
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•20•7•0•Updated Aug 6, 2024Aug 6, 2024
metMHN
Public
This is a adaptation to MHN so that it works on metastasis
cancer-genomics
Python
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MIT License
•3•4•0•0•Updated Jul 13, 2024Jul 13, 2024
BnpC
Public
Bayesian non-parametric clustering (BnpC) of binary data with missing values and uneven error rates
binary-data clustering mcmc genotyping split-merge
Python
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MIT License
•4•18•8•0•Updated Jul 11, 2024Jul 11, 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 Jul 8, 2024Jul 8, 2024
covvfit
Public
Fitness estimates of SARS-CoV-2 variants
epidemiology bayesian-statistics fitness-landscape sars-cov-2
Python
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MIT License
•0•0•0•0•Updated Jun 5, 2024Jun 5, 2024