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    49 repositories

    • BMBL-analysis-notebooks

      Public
      A collection of bioinformatics data analysis notebooks focused on providing examples of current best practices in single-cell analysis.
      HTML
      •8•12•0•0•Updated Jan 20, 2025Jan 20, 2025

    • marsgt

      Public
      Multi-omics data analysis for rare population inference using single-cell graph transformer
      Jupyter Notebook
      •3•17•3•0•Updated Nov 23, 2024Nov 23, 2024

    • SQUAD

      Public
      Spatial QUality Assessment and Diagnosis
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • scGNN-frontend

      Public
      a typescript frontend for scGNN
      TypeScript
      •
      MIT License
      •2•0•0•0•Updated Oct 3, 2024Oct 3, 2024

    • SpaGFT

      Public
      Detect
      Jupyter Notebook
      •
      MIT License
      •3•4•0•0•Updated Aug 29, 2024Aug 29, 2024

    • scDEAL

      Public
      Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-seq data
      Jupyter Notebook
      •
      Apache License 2.0
      •13•50•15•0•Updated Jul 22, 2024Jul 22, 2024

    • STREAM

      Public
      STREAM: enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data
      single-cellgene-regulatory-networkmultiomics
      R
      •
      Other
      •1•0•2•0•Updated Jul 18, 2024Jul 18, 2024

    • ssread

      Public
      A single-cell and spatial RNA-seq database for Alzheimer’s Disease
      Vue
      •
      MIT License
      •7•21•0•0•Updated Jul 17, 2024Jul 17, 2024

    • Spinal-cord-scRNAseq

      Public
      Supplementary code for the analyses presented in the manuscript: Microglia coordinate intracellular interactions during spinal cord repair in mice
      HTML
      •2•3•0•0•Updated Jul 2, 2024Jul 2, 2024

    • tesa

      Public
      C
      •1•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • scGNN2.0

      Public
      Jupyter Notebook
      •
      MIT License
      •0•11•4•0•Updated Dec 4, 2023Dec 4, 2023

    • CEMIG

      Public
      A new motif prediction algorithm called CEMIG (cis regulatory motif influence using de Bruijn graph)
      C++
      •3•1•0•0•Updated Nov 26, 2023Nov 26, 2023

    • deepmaps

      Public
      Single-cell biological network inference using a heterogeneous graph transformer
      HTML
      •6•69•5•1•Updated Oct 29, 2023Oct 29, 2023

    • stream_analyses

      Public
      R
      •0•0•1•0•Updated Aug 20, 2023Aug 20, 2023

    • BMBL-Tutorial-SOP

      Public
      0•0•0•0•Updated Aug 16, 2023Aug 16, 2023

    • IDAM

      Public
      Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data
      C
      •1•3•0•0•Updated Aug 15, 2023Aug 15, 2023

    • scread-backend

      Public
      JavaScript
      •
      MIT License
      •3•5•0•18•Updated Jul 10, 2023Jul 10, 2023

    • DESSO

      Public
      A DL-based framework for sequence and shape motif identification in the human genome
      MATLAB
      •9•9•1•1•Updated May 26, 2023May 26, 2023

    • NOTCH1-cardiac-lineage-scRNAseq

      Public
      Impaired Human Cardiac Cell Development due to NOTCH1 Deficiency
      HTML
      •1•2•0•0•Updated May 18, 2023May 18, 2023

    • MEGA

      Public
      a deep learning-based python package for identifying cancer-associated intratumoral microbes.
      Python
      •
      MIT License
      •0•2•0•0•Updated Apr 14, 2023Apr 14, 2023

    • IRIS3

      Public
      IRIS3: Integrated Cell-type-specific Regulon Inference Server from Single-cell RNA-Seq (https://bmbl.bmi.osumc.edu/iris3/)
      JavaScript
      •
      GNU General Public License v3.0
      •1•10•1•0•Updated Mar 21, 2023Mar 21, 2023

    • micah

      Public
      Python
      •1•0•0•0•Updated Mar 11, 2023Mar 11, 2023

    • AD-spatial-code

      Public
      Code for manuscript "Spatially resolved transcriptomics reveals gene signatures underlying the vulnerability of 2 human middle temporal gyrus in Alzheimer's disease"
      R
      •1•1•0•0•Updated Jan 8, 2023Jan 8, 2023

    • bmbl-class-notebooks

      Public
      HTML
      •4•2•0•0•Updated Oct 11, 2022Oct 11, 2022

    • BMI8130-notebooks-2021

      Public
      HTML
      •4•1•0•0•Updated Jul 27, 2022Jul 27, 2022

    • RESEPT

      Public
      A deep-learning framework for characterizing and visualizing tissue architecture from spatially resolved transcriptomics
      Python
      •
      MIT License
      •6•8•0•0•Updated Jul 11, 2022Jul 11, 2022

    • IOM

      Public
      Python
      •1•1•0•0•Updated Jul 9, 2022Jul 9, 2022

    • scread-protocol

      Public
      R
      •2•16•0•1•Updated Jul 3, 2022Jul 3, 2022

    • IRISFGM

      Public
      Development repository for the IRISFGM package for submission purposes
      R
      •4•0•0•0•Updated Aug 21, 2021Aug 21, 2021

    • deepmotif-benchmark

      Public
      0•4•0•0•Updated May 10, 2021May 10, 2021