Repositories list

• GeneICL

  Public
  A tabular foundation model for bulk transcriptomics

  Python

  •

  MIT License

  •00 forks in BoevaLab/GeneICL•22 stars in BoevaLab/GeneICL•00 issues in BoevaLab/GeneICL•00 pull requests in BoevaLab/GeneICL•Updated Oct 30, 2026Oct 30, 2026

• Chiron3D

  Public
  An interpretable deep learning framework for understanding the DNA code of chromatin looping

  Jupyter Notebook

  •

  MIT License

  •22 forks in BoevaLab/Chiron3D•33 stars in BoevaLab/Chiron3D•00 issues in BoevaLab/Chiron3D•00 pull requests in BoevaLab/Chiron3D•Updated Oct 28, 2026Oct 28, 2026

• Gene-Embedding-Hub

  Public
  Python

  •00 forks in BoevaLab/Gene-Embedding-Hub•00 stars in BoevaLab/Gene-Embedding-Hub•00 issues in BoevaLab/Gene-Embedding-Hub•00 pull requests in BoevaLab/Gene-Embedding-Hub•Updated Oct 27, 2026Oct 27, 2026

• sae-for-scFMs

  Public
  Python

  •00 forks in BoevaLab/sae-for-scFMs•55 stars in BoevaLab/sae-for-scFMs•00 issues in BoevaLab/sae-for-scFMs•00 pull requests in BoevaLab/sae-for-scFMs•Updated Oct 27, 2026Oct 27, 2026

• grass-mil

  Public
  Code repository containing the code for the "GRASS-MIL" method

  Jupyter Notebook

  •

  MIT License

  •22 forks in BoevaLab/grass-mil•44 stars in BoevaLab/grass-mil•00 issues in BoevaLab/grass-mil•33 pull requests in BoevaLab/grass-mil•Updated Oct 16, 2026Oct 16, 2026

• ASAP

  Public
  Early feature extraction determines performance: systematic evaluation of deep learning models for high-resolution chromatin accessibility prediction

  Jupyter Notebook

  •

  MIT License

  •11 fork in BoevaLab/ASAP•55 stars in BoevaLab/ASAP•00 issues in BoevaLab/ASAP•11 pull request in BoevaLab/ASAP•Updated Aug 24, 2026Aug 24, 2026

• CDState

  Public
  CDState: An unsupervised approach to predict malignant cell heterogeneity in tumor bulk RNA-sequencing data

  Jupyter Notebook

  •

  MIT License

  •00 forks in BoevaLab/CDState•66 stars in BoevaLab/CDState•11 issue in BoevaLab/CDState•00 pull requests in BoevaLab/CDState•Updated Jul 29, 2026Jul 29, 2026

• scSSL-Bench

  Public
  Python

  •00 forks in BoevaLab/scSSL-Bench•1212 stars in BoevaLab/scSSL-Bench•22 issues in BoevaLab/scSSL-Bench•00 pull requests in BoevaLab/scSSL-Bench•Updated Jun 21, 2026Jun 21, 2026

• UniversalEPI

  Public
  UniversalEPI: Harnessing Attention Mechanisms to Decode Chromatin Interactions in Rare and Unexplored Cell Types

  Jupyter Notebook

  •

  MIT License

  •00 forks in BoevaLab/UniversalEPI•77 stars in BoevaLab/UniversalEPI•00 issues in BoevaLab/UniversalEPI•00 pull requests in BoevaLab/UniversalEPI•Updated May 27, 2026May 27, 2026

• ANS_signature_scoring

  Public
  ANS_signature_scoring: A gene expression signature scoring Python package.

  Python

  •

  MIT License

  •33 forks in BoevaLab/ANS_signature_scoring•2020 stars in BoevaLab/ANS_signature_scoring•11 issue in BoevaLab/ANS_signature_scoring•00 pull requests in BoevaLab/ANS_signature_scoring•Updated Jan 18, 2026Jan 18, 2026

• ANS_supplementary_information

  Public
  Jupyter Notebook

  •00 forks in BoevaLab/ANS_supplementary_information•00 stars in BoevaLab/ANS_supplementary_information•00 issues in BoevaLab/ANS_supplementary_information•00 pull requests in BoevaLab/ANS_supplementary_information•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

  •00 forks in BoevaLab/DeepCAST-GWAS•11 star in BoevaLab/DeepCAST-GWAS•00 issues in BoevaLab/DeepCAST-GWAS•00 pull requests in BoevaLab/DeepCAST-GWAS•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

  •1313 forks in BoevaLab/ONCOCNV•2626 stars in BoevaLab/ONCOCNV•1414 issues in BoevaLab/ONCOCNV•11 pull request in BoevaLab/ONCOCNV•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

  •00 forks in BoevaLab/spatial-augmentations•11 star in BoevaLab/spatial-augmentations•55 issues in BoevaLab/spatial-augmentations•55 pull requests in BoevaLab/spatial-augmentations•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

  •11 fork in BoevaLab/CanSig-benchmark•66 stars in BoevaLab/CanSig-benchmark•11 issue in BoevaLab/CanSig-benchmark•00 pull requests in BoevaLab/CanSig-benchmark•Updated Oct 10, 2025Oct 10, 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

  •99 forks in BoevaLab/CancerFoundation•3232 stars in BoevaLab/CancerFoundation•11 issue in BoevaLab/CancerFoundation•00 pull requests in BoevaLab/CancerFoundation•Updated Sep 12, 2025Sep 12, 2025

• survboard

  Public
  Python

  •

  MIT License

  •00 forks in BoevaLab/survboard•1010 stars in BoevaLab/survboard•00 issues in BoevaLab/survboard•00 pull requests in BoevaLab/survboard•Updated Aug 1, 2025Aug 1, 2025

• hierarchical-spatial-classifier

  Public
  Jupyter Notebook

  •11 fork in BoevaLab/hierarchical-spatial-classifier•00 stars in BoevaLab/hierarchical-spatial-classifier•00 issues in BoevaLab/hierarchical-spatial-classifier•00 pull requests in BoevaLab/hierarchical-spatial-classifier•Updated Jul 28, 2025Jul 28, 2025

• GWAS-power

  Public
  Jupyter Notebook

  •00 forks in BoevaLab/GWAS-power•00 stars in BoevaLab/GWAS-power•00 issues in BoevaLab/GWAS-power•00 pull requests in BoevaLab/GWAS-power•Updated Jul 17, 2025Jul 17, 2025

• perturbench

  Public
  Jupyter Notebook

  •

  Other

  •1616 forks in BoevaLab/perturbench•00 stars in BoevaLab/perturbench•00 issues in BoevaLab/perturbench•11 pull request in BoevaLab/perturbench•Updated Jul 8, 2025Jul 8, 2025

• Dhaka-implementation

  Public
  Python

  •00 forks in BoevaLab/Dhaka-implementation•00 stars in BoevaLab/Dhaka-implementation•00 issues in BoevaLab/Dhaka-implementation•00 pull requests in BoevaLab/Dhaka-implementation•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

  •11 fork in BoevaLab/MTRNA-sc-cancer•11 star in BoevaLab/MTRNA-sc-cancer•00 issues in BoevaLab/MTRNA-sc-cancer•00 pull requests in BoevaLab/MTRNA-sc-cancer•Updated Mar 18, 2025Mar 18, 2025

• single-cell-transformer-papers

  Public
  HTML

  •

  Other

  •4141 forks in BoevaLab/single-cell-transformer-papers•00 stars in BoevaLab/single-cell-transformer-papers•00 issues in BoevaLab/single-cell-transformer-papers•00 pull requests in BoevaLab/single-cell-transformer-papers•Updated Dec 19, 2024Dec 19, 2024

• scAugmentBench

  Public
  Benchmarking Self-Supervised Learning for Single-Cell Data

  Python

  •00 forks in BoevaLab/scAugmentBench•77 stars in BoevaLab/scAugmentBench•00 issues in BoevaLab/scAugmentBench•00 pull requests in BoevaLab/scAugmentBench•Updated Oct 28, 2024Oct 28, 2024

• FREEC

  Public
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

  C++

  •5151 forks in BoevaLab/FREEC•180180 stars in BoevaLab/FREEC•9898 issues in BoevaLab/FREEC•1111 pull requests in BoevaLab/FREEC•Updated Aug 22, 2024Aug 22, 2024

• sparsesurv

  Public
  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork in BoevaLab/sparsesurv•33 stars in BoevaLab/sparsesurv•77 issues in BoevaLab/sparsesurv•11 pull request in BoevaLab/sparsesurv•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

  •3232 forks in BoevaLab/infercnvpy•11 star in BoevaLab/infercnvpy•00 issues in BoevaLab/infercnvpy•22 pull requests in BoevaLab/infercnvpy•Updated May 21, 2024May 21, 2024

• scalop

  Public
  Single Cell Analysis Operations

  R

  •

  MIT License

  •2828 forks in BoevaLab/scalop•11 star in BoevaLab/scalop•00 issues in BoevaLab/scalop•00 pull requests in BoevaLab/scalop•Updated May 16, 2024May 16, 2024

• nsclc_patterns

  Public
  00 forks in BoevaLab/nsclc_patterns•00 stars in BoevaLab/nsclc_patterns•00 issues in BoevaLab/nsclc_patterns•00 pull requests in BoevaLab/nsclc_patterns•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

  •00 forks in BoevaLab/CRCPolyp•00 stars in BoevaLab/CRCPolyp•00 issues in BoevaLab/CRCPolyp•00 pull requests in BoevaLab/CRCPolyp•Updated Feb 20, 2024Feb 20, 2024