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    37 repositories

    • GWAS-power

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 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
      •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

    • CancerFoundation

      Public
      CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
      cancersingle-cellfoundation-model
      Jupyter Notebook
      •
      MIT License
      •1•13•0•0•Updated Feb 4, 2025Feb 4, 2025

    • ANS_supplementary_information

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 30, 2025Jan 30, 2025

    • CanSig-benchmark

      Public
      CanSig: a package to compare methods for discovering shared transcriptional states in cancer.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • UniversalEPI

      Public
      UniversalEPI: Harnessing Attention Mechanisms to Decode Chromatin Interactions in Rare and Unexplored Cell Types
      Python
      •
      MIT License
      •0•1•0•0•Updated Jan 26, 2025Jan 26, 2025

    • single-cell-transformer-papers

      Public
      HTML
      •
      Other
      •38•0•0•0•Updated Dec 19, 2024Dec 19, 2024

    • scAugmentBench

      Public
      Benchmarking Self-Supervised Learning for Single-Cell Data
      Python
      •0•5•0•0•Updated Oct 28, 2024Oct 28, 2024

    • survboard

      Public
      R
      •
      MIT License
      •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++
      •50•157•90•10•Updated Aug 22, 2024Aug 22, 2024

    • sparsesurv

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•6•0•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
      •27•1•0•1•Updated May 21, 2024May 21, 2024

    • scalop

      Public
      Single Cell Analysis Operations
      R
      •
      MIT License
      •23•0•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
      •6•7•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•7•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•4•0•0•Updated May 16, 2023May 16, 2023

    • LILY

      Public
      Detection of super-enhancers in cancer data
      R
      •9•20•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

    • HongzheLabro

      Public
      This is the code collection for Hongzhe Li's Lab rotation project
      Jupyter Notebook
      •0•0•0•0•Updated Jan 3, 2023Jan 3, 2023

    • latte

      Public
      Data analysis of latent representations
      Python
      •
      MIT License
      •1•3•1•1•Updated Dec 30, 2022Dec 30, 2022

    • ONCOCNV

      Public
      ONCOCNV - a package to detect copy number changes in Targeted Deep Sequencing and Exome-seq data
      R
      •12•25•14•1•Updated Nov 2, 2022Nov 2, 2022

    • TFCox

      Public
      Tensorflow implementation of the Cox Proportional Hazards model
      Jupyter Notebook
      •0•1•0•0•Updated Jun 9, 2022Jun 9, 2022

    • CIMP_etiology_oncogenic_transformation

      Public
      Supporting code for the analysis in "Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype (CIMP): a pan-cancer analysis
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Feb 23, 2022Feb 23, 2022

    • QuantumClone

      Public
      Clonal reconstruction from HTS data
      R
      •6•0•0•0•Updated Oct 26, 2021Oct 26, 2021

    • Group_Lasso_and_Multitask

      Public
      Python
      •1•1•0•0•Updated Sep 2, 2021Sep 2, 2021

    • Multi-task-Side-Channel

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 16, 2020Nov 16, 2020