Repositories list

• SpaMosaic

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• DISCOtoolkit_py

  Public
  Python version of DISCO toolkit

  rna-seqsinglecellatlas-data

  Python

  •1•12•2•0•Updated Nov 21, 2024Nov 21, 2024

• SEDR

  Public
  Python

  •

  MIT License

  •10•49•5•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

  R

  •4•23•2•0•Updated Oct 25, 2024Oct 25, 2024

• DISCOtoolkit

  Public
  R

  •4•27•0•0•Updated Oct 24, 2024Oct 24, 2024

• SpatialGlue

  Public
  SpatialGlue is a novel deep learning methods for spatial multi-omics data integration.

  Python

  •

  GNU Affero General Public License v3.0

  •8•44•17•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•1•0•0•Updated Jun 22, 2024Jun 22, 2024

• SpatialGlue_3M

  Public
  Extended version of SpatialGlue for integration of spatial triplet modality data.

  Python

  •0•4•0•0•Updated Jun 22, 2024Jun 22, 2024

• NNI_brain_code

  Public
  R

  •0•1•0•0•Updated May 3, 2024May 3, 2024

• scTM

  Public
  scTM: A package for topic modelling in transcriptomics data

  Python

  •0•9•10•0•Updated May 1, 2024May 1, 2024

• GraphST

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •14•99•32•1•Updated Mar 19, 2024Mar 19, 2024

• SpatialGlue_notebook

  Public
  Jupyter Notebook

  •0•3•3•0•Updated Mar 5, 2024Mar 5, 2024

• ezSingleCell2

  Public
  R

  •

  GNU General Public License v3.0

  •6•50•5•0•Updated Jan 2, 2024Jan 2, 2024

• SEDR_analyses

  Public
  R

  •17•37•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•2•0•Updated Mar 8, 2023Mar 8, 2023

• Bone_Marrow_Aging

  Public
  R

  •0•3•0•0•Updated Feb 28, 2023Feb 28, 2023

• cytofkit2

  Public
  R

  •15•22•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

  •46•73•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

  •692•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•57•63•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

  •26•47•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