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@BoevaLab Boeva Lab, ETH Zurich

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    48 repositories

    • ASAP

      Public
      Early feature extraction determines performance: systematic evaluation of deep learning models for high-resolution chromatin accessibility prediction
      Jupyter Notebook
      •
      MIT License
      •1•3•2•0•Updated Apr 14, 2026Apr 14, 2026

    • UniversalEPI

      Public
      UniversalEPI: Harnessing Attention Mechanisms to Decode Chromatin Interactions in Rare and Unexplored Cell Types
      Jupyter Notebook
      •
      MIT License
      •0•5•0•0•Updated Apr 10, 2026Apr 10, 2026

    • sae-for-scFMs

      Public
      Python
      •0•1•0•0•Updated Apr 7, 2026Apr 7, 2026

    • Chiron3D

      Public
      An interpretable deep learning framework for understanding the DNA code of chromatin looping
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Mar 28, 2026Mar 28, 2026

    • CDState

      Public
      Python
      •
      MIT License
      •0•3•0•0•Updated Feb 18, 2026Feb 18, 2026

    • ANS_signature_scoring

      Public
      ANS_signature_scoring: A gene expression signature scoring Python package.
      Python
      •
      MIT License
      •3•18•1•0•Updated Jan 18, 2026Jan 18, 2026

    • ANS_supplementary_information

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 18, 2026Jan 18, 2026

    • DeepCAST-GWAS

      Public
      This is the repository hosting all the source code of the DeepCAST-GWAS method.
      Jupyter Notebook
      •0•1•0•0•Updated Jan 6, 2026Jan 6, 2026

    • ONCOCNV

      Public
      ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data
      R
      •13•25•14•1•Updated Oct 30, 2025Oct 30, 2025

    • 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
      •1•5•1•0•Updated Oct 10, 2025Oct 10, 2025

    • scSSL-Bench

      Public
      Python
      •0•11•1•0•Updated Oct 3, 2025Oct 3, 2025

    • CancerFoundation

      Public
      CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
      cancersingle-cellfoundation-model
      cancersingle-cellfoundation-model
      Jupyter Notebook
      •
      MIT License
      •6•29•1•0•Updated Sep 12, 2025Sep 12, 2025

    • survboard

      Public
      Python
      •
      MIT License
      •0•8•0•0•Updated Aug 1, 2025Aug 1, 2025

    • hierarchical-spatial-classifier

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

    • GWAS-power

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

    • perturbench

      Public
      Jupyter Notebook
      •
      Other
      •15•0•0•1•Updated Jul 8, 2025Jul 8, 2025

    • Dhaka-implementation

      Public
      Python
      •0•0•0•0•Updated Jul 2, 2025Jul 2, 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 ma…
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Mar 18, 2025Mar 18, 2025

    • single-cell-transformer-papers

      Public
      HTML
      •
      Other
      •41•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • scAugmentBench

      Public
      Benchmarking Self-Supervised Learning for Single-Cell Data
      Python
      •0•7•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++
      •50•178•98•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
      •32•1•0•2•Updated May 21, 2024May 21, 2024

    • scalop

      Public
      Single Cell Analysis Operations
      R
      •
      MIT License
      •27•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
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