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    35 repositories

    • SpaMosaic

      Public
      Python
      •
      MIT License
      •2•8•0•0•Updated Jan 28, 2026Jan 28, 2026

    • NNI_paper

      Public
      R
      •0•1•0•0•Updated Jul 16, 2025Jul 16, 2025

    • DISCOtoolkit_py

      Public
      Python version of DISCO toolkit
      rna-seqsinglecellatlas-data
      rna-seqsinglecellatlas-data
      Python
      •1•12•2•0•Updated Nov 21, 2024Nov 21, 2024

    • SEDR

      Public
      Python
      •
      MIT License
      •11•69•10•0•Updated Nov 6, 2024Nov 6, 2024

    • FastIntegration

      Public
      FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
      discodata-integrationsingle-cell
      discodata-integrationsingle-cell
      R
      •5•23•2•0•Updated Oct 25, 2024Oct 25, 2024

    • SpatialGlue

      Public
      SpatialGlue is a novel deep learning methods for spatial multi-omics data integration.
      Python
      •
      GNU Affero General Public License v3.0
      •11•86•38•0•Updated Jun 24, 2024Jun 24, 2024

    • SpatialGlue_tutorials

      Public
      The tutorial is to show how to apply SpatialGlue to integrate spatial multi-omics data to decipher tissue heterogeneity.
      Python
      •0•3•0•0•Updated Jun 22, 2024Jun 22, 2024

    • SpatialGlue_3M

      Public
      Extended version of SpatialGlue for integration of spatial triplet modality data.
      Python
      •0•6•0•0•Updated Jun 22, 2024Jun 22, 2024

    • NNI_brain_code

      Public
      R
      •0•2•0•0•Updated May 3, 2024May 3, 2024

    • scTM

      Public
      scTM: A package for topic modelling in transcriptomics data
      Python
      •2•24•12•0•Updated May 1, 2024May 1, 2024

    • GraphST

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •24•154•45•1•Updated Mar 19, 2024Mar 19, 2024

    • SpatialGlue_notebook

      Public
      Jupyter Notebook
      •2•7•6•0•Updated Mar 5, 2024Mar 5, 2024

    • ezSingleCell2

      Public
      R
      •
      GNU General Public License v3.0
      •7•59•5•0•Updated Jan 2, 2024Jan 2, 2024

    • SEDR_analyses

      Public
      R
      •17•41•5•1•Updated Dec 4, 2023Dec 4, 2023

    • GENEX

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 6, 2023Nov 6, 2023

    • GraphST_Tutorials

      Public
      Python
      •2•2•3•0•Updated Mar 8, 2023Mar 8, 2023

    • Bone_Marrow_Aging

      Public
      R
      •0•6•0•0•Updated Feb 28, 2023Feb 28, 2023

    • cytofkit2

      Public
      R
      •15•25•46•1•Updated May 7, 2022May 7, 2022

    • Batch-effect-removal-benchmarking

      Public
      A benchmark of batch-effect correction methods for single-cell RNA sequencing data
      Jupyter Notebook
      •49•79•13•0•Updated Jan 24, 2022Jan 24, 2022

    • MCGC

      Public
      Python
      •11•0•0•0•Updated Dec 10, 2021Dec 10, 2021

    • pyGAT

      Public
      Pytorch implementation of the Graph Attention Network model by Veličković et. al (2017, https://arxiv.org/abs/1710.10903)
      Python
      •
      MIT License
      •702•0•0•0•Updated Aug 15, 2021Aug 15, 2021

    • cytofkit2-1

      Public
      R
      •3•0•0•1•Updated Apr 22, 2021Apr 22, 2021

    • cytofkit

      Public
      cytofkit: an integrated flow/mass cytometry data analysis pipeline
      R
      •27•61•64•4•Updated Dec 17, 2020Dec 17, 2020

    • oneSENSE

      Public
      R
      •
      GNU General Public License v3.0
      •3•0•6•1•Updated Jun 23, 2020Jun 23, 2020

    • Rphenograph

      Public
      Rphenograph: R implementation of the PhenoGraph algorithm
      R
      •29•52•9•5•Updated Jun 8, 2020Jun 8, 2020

    • Harmony

      Public
      R
      •1•2•2•0•Updated Feb 12, 2019Feb 12, 2019

    • ezSingleCell

      Public
      GUI implementation for Seurat using shiny
      R
      •3•6•0•0•Updated Apr 20, 2018Apr 20, 2018

    • CycleX

      Public
      Scripts to reproduce Yong Kee's Thesis
      0•0•0•0•Updated Nov 2, 2017Nov 2, 2017

    • SC-QC

      Public
      Quality control for Single-cell RNA-seq data
      R
      •1•0•0•0•Updated Oct 13, 2017Oct 13, 2017

    • uSORT

      Public
      uSORT: A self-refining ordering pipeline for gene selection
      R
      •0•1•0•0•Updated Oct 12, 2016Oct 12, 2016
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