Repositories list

• oncotreeVIS

  Public
  An interactive graphical user interface for visualizing mutation tree cohorts.

  JavaScript

  •

  MIT License

  •0•0•0•0•Updated Apr 12, 2025Apr 12, 2025

• WisePulse

  Public
  WISE Loculus with V-Pipe – Infra for start-to-end viral wastewater analysis.

  Rust

  •

  MIT License

  •0•1•1•1•Updated Apr 11, 2025Apr 11, 2025

• sr2silo

  Public
  Wrangling short-read sequencing data for import into SILO

  Python

  •

  MIT License

  •0•1•14•3•Updated Apr 10, 2025Apr 10, 2025

• vpipe-biohack24-frontend

  Public
  Cloudification of V-Pipe: Frontend for the Biohackathon 2024

  biohackeu24elixir-cloud-aai

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• V-pipe

  Public
  V-pipe is a pipeline designed for analysing NGS data of short viral genomes

  snakemakevirussequencing+ 12condabioinformatics-pipelinehivsars-cov-2sarscov2biohackeu20biohackcovid20+ 5

  Jupyter Notebook

  •

  Apache License 2.0

  •46•135•34•3•Updated Apr 9, 2025Apr 9, 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•19•5•0•Updated Apr 8, 2025Apr 8, 2025

• pangolin

  Public
  BSSE COVID-19 sequencing of test swab samples

  Shell

  •3•7•1•0•Updated Apr 8, 2025Apr 8, 2025

• RSV-wastewater-V-pipe

  Public
  Wastewater-derived Respiratory Syncytial Virus data analysis

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

• mt-SCITE

  Public
  Tree inference from mitochondrial mutations

  Jupyter Notebook

  •1•5•0•0•Updated Apr 4, 2025Apr 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 Apr 4, 2025Apr 4, 2025

• oncotree2vec

  Public
  A method for embedding and clustering of tumor mutation trees.

  Python

  •0•8•0•0•Updated Apr 4, 2025Apr 4, 2025

• Influenza_wastewater_analysis

  Public
  R

  •0•0•6•0•Updated Apr 3, 2025Apr 3, 2025

• Jnotype

  Public
  Probabilistic modeling of high-dimensional binary data in JAX

  clusteringcancer-genomicsunsupervised-learning+ 4bayesian-statisticsjaxprobabilistic-machine-learningideal-point-estimation

  Python

  •

  Other

  •0•3•6•2•Updated Apr 1, 2025Apr 1, 2025

• LongSom

  Public
  LongSom tool for long-reads

  Python

  •0•8•3•0•Updated Apr 1, 2025Apr 1, 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 Apr 1, 2025Apr 1, 2025

• covvfit

  Public
  Fitness estimates of SARS-CoV-2 variants

  epidemiologyforecasting-modelsfitness-landscape+ 5virologystatistical-modelingsars-cov-2wastewater-surveillancewastewater-based-epidemiology

  Python

  •

  MIT License

  •0•1•6•2•Updated Mar 29, 2025Mar 29, 2025

• FiTree

  Public
  FiTree: Bayesian inference of fitness landscapes via tree-structured branching processes

  Jupyter Notebook

  •

  MIT License

  •0•3•0•0•Updated Mar 28, 2025Mar 28, 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•2•3•0•Updated Mar 28, 2025Mar 28, 2025

• LolliPop

  Public
  Deconvolution for Wastewater Genomics

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•3•2•1•Updated Mar 28, 2025Mar 28, 2025

• DCV-CrPV-cGAS-STING-pathway-data-analysis

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Mar 26, 2025Mar 26, 2025

• pMHN

  Public
  Personalised mutual hazard networks: fixed effects in cancer progression modeling

  probabilistic-modelscancer-evolution

  Python

  •

  MIT License

  •0•3•1•0•Updated Mar 22, 2025Mar 22, 2025

• cowwid

  Public
  Procedure used fro the surveillance of SARS-CoV-2 genomic variants in wastewater.

  covid-19sars-cov-2bioinformatics+ 2pipelinengs

  Jupyter Notebook

  •

  Other

  •0•7•1•0•Updated Mar 10, 2025Mar 10, 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

• 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

• lollipop-in-cloud

  Public
  On the fly variant deconvolution running in the cloud for on demand user requests.

  biohackeu24elixir-cloud-aai

  Python

  •0•0•0•0•Updated Feb 10, 2025Feb 10, 2025

• bmi

  Public
  Mutual information estimators and benchmark

  pythonbenchmarkestimator+ 1mutual-information

  Python

  •

  MIT License

  •6•48•8•2•Updated Jan 18, 2025Jan 18, 2025

• demoTape

  Public
  Computational demultiplexing of targeted single-cell sequencing (tapestri) data

  Python

  •

  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-genomicsbayesian-inferencemcmc+ 2single-cellcopy-number-variation

  C++

  •

  GNU General Public License v3.0

  •8•23•7•0•Updated Dec 21, 2024Dec 21, 2024

• GSoD-2024

  Public
  Google Season of Docs 2024

  0•1•0•0•Updated Dec 10, 2024Dec 10, 2024