Skip to content

@BoevaLab Boeva Lab, ETH Zurich

Change the repository type filter

All

    Repositories list

    45 repositories

    • spatial-augmentations

      Public
      Graph augmentation strategies for self-supervised pretraining of graph neural networks in spatial omics
      Python
      •
      MIT License
      •0•1•5•5•Updated Oct 26, 2025Oct 26, 2025

    • CanSig-benchmark

      Public
      CanSig: a package to compare methods for discovering shared transcriptional states in cancer.
      Jupyter Notebook
      •
      MIT License
      •0•2•1•0•Updated Oct 10, 2025Oct 10, 2025

    • scSSL-Bench

      Public
      Python
      •0•10•0•0•Updated Oct 3, 2025Oct 3, 2025

    • ANS_supplementary_information

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 1, 2025Oct 1, 2025

    • ANS_signature_scoring

      Public
      ANS_signature_scoring: A gene expression signature scoring Python package.
      Python
      •
      MIT License
      •3•16•1•0•Updated Sep 20, 2025Sep 20, 2025

    • CancerFoundation

      Public
      CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
      cancersingle-cellfoundation-model
      Jupyter Notebook
      •
      MIT License
      •4•25•1•0•Updated Sep 12, 2025Sep 12, 2025

    • survboard

      Public
      Python
      •
      MIT License
      •0•7•0•0•Updated Aug 1, 2025Aug 1, 2025

    • hierarchical-spatial-classifier

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • UniversalEPI

      Public
      UniversalEPI: Harnessing Attention Mechanisms to Decode Chromatin Interactions in Rare and Unexplored Cell Types
      Jupyter Notebook
      •
      MIT License
      •0•4•0•0•Updated Jul 19, 2025Jul 19, 2025

    • GWAS-power

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 17, 2025Jul 17, 2025

    • perturbench

      Public
      Jupyter Notebook
      •
      Other
      •7•0•0•1•Updated Jul 8, 2025Jul 8, 2025

    • Dhaka-implementation

      Public
      Python
      •0•0•0•0•Updated Jul 2, 2025Jul 2, 2025

    • ASAP

      Public
      Early feature extraction determines performance: systematic evaluation of deep learning models for high-resolution chromatin accessibility prediction
      Python
      •
      MIT License
      •1•2•1•0•Updated Jun 17, 2025Jun 17, 2025

    • CDState

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated May 13, 2025May 13, 2025

    • MTRNA-sc-cancer

      Public
      Repository containing all the code necessary for reproducing the paper "Filtering cells with high mitochondrial content removes viable metabolically altered malignant cell populations in cancer single-cell studies" (Yates, Kraft, and Boeva)
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 18, 2025Mar 18, 2025

    • single-cell-transformer-papers

      Public
      HTML
      •
      Other
      •40•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • scAugmentBench

      Public
      Benchmarking Self-Supervised Learning for Single-Cell Data
      Python
      •0•6•0•0•Updated Oct 28, 2024Oct 28, 2024

    • FREEC

      Public
      Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
      C++
      •51•172•93•10•Updated Aug 22, 2024Aug 22, 2024

    • sparsesurv

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•7•1•Updated Jul 16, 2024Jul 16, 2024

    • infercnvpy

      Public
      Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •30•1•0•2•Updated May 21, 2024May 21, 2024

    • scalop

      Public
      Single Cell Analysis Operations
      R
      •
      MIT License
      •26•1•0•0•Updated May 16, 2024May 16, 2024

    • nsclc_patterns

      Public
      0•0•0•0•Updated Apr 15, 2024Apr 15, 2024

    • CRCPolyp

      Public
      Supporting code for Identification of early DNA methylation field cancerization in normal colonic mucosa in patients with adenomas and neoplastic lesions
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • CHIPIN

      Public
      ChIP-seq Intersample Normalization
      R
      •
      GNU General Public License v3.0
      •5•8•5•1•Updated Feb 1, 2024Feb 1, 2024

    • Multi-omics-noise-resistance

      Public
      More data, more problems? On noise resistance in multi-omics cancer survival models
      Python
      •
      MIT License
      •2•9•0•0•Updated Jul 29, 2023Jul 29, 2023

    • HMCan

      Public
      C++
      •3•7•1•0•Updated Jun 9, 2023Jun 9, 2023

    • Teaching

      Public
      Teaching materials
      Jupyter Notebook
      •0•5•0•0•Updated May 16, 2023May 16, 2023

    • LILY

      Public
      Detection of super-enhancers in cancer data
      R
      •9•21•0•1•Updated Apr 10, 2023Apr 10, 2023

    • CanSig-Supplementary-Information

      Public
      This repository supplements the CanSig tool (https://github.com/boevaLab/cansig), providing additional information on performed experiments.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Mar 27, 2023Mar 27, 2023

    • SplatterSim

      Public
      a package to simulate cancer single cells with joint CNV profiles based on Splatter
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 17, 2023Jan 17, 2023