scGEAToolbox (single-cell Gene Expression Analysis Toolbox)

Version 25.9.0 (302 MB) by James Cai
Single-cell Gene Expression Analysis Toolbox
5.0
(2)
1.4K Downloads
Updated 4 Sep 2025
View License on GitHub

Cite As

Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics. 2019 Nov 7:btz830. doi: 10.1093/bioinformatics/btz830. PMID: 31697351.

MATLAB Release Compatibility
Created with R2024b
Compatible with R2014b and later releases
Platform Compatibility
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+gui

+gui/private

+llm

+pkg

+pkg/private

+qtm

+run

+run/private

+ten

@SingleCellExperiment

doc/mlx

external/R_Seurat

external/R_SeuratSaveRds

external/R_clustermole

external/fun_MPPC

external/fun_alona_panglaodb

external/fun_alona_subtypes

external/fun_kNNcode

external/fun_locfit

external/ml_ComBat

external/ml_GENIE3

external/ml_GENIE3/RT

external/ml_MAGIC

external/ml_PHATE

external/ml_SC3/ClusterPack

external/ml_SIMLR

external/ml_SIMLR/src

external/ml_SNNDPC

external/ml_SinNLRR

external/ml_SoptSC

external/ml_SoptSC/NNDSVD

external/ml_SoptSC/symnmf2

external/ml_SoptSC/vinlinplot

external/ml_Specter

external/ml_Specter/LSC

external/ml_Specter/dimred

external/ml_Specter/utils

external/ml_UMAP44

external/ml_UMAP44/util

external/ml_cbrewer

external/ml_scGeneFit

external/ml_scGeneFit/source

external/ml_scGeneFit/source/classification_metrics

external/ml_umap45

external/ml_umap45/util

external/py_harmonypy

external/py_panhumanpy

external/py_scimilarity

external/py_scrublet

external/py_writeh5ad

external/quantum/gate

external/quantum/gate/+quantum/+gate

external/quantum/gate/+quantum/+internal/+gate

external/quantum/gate/+quantum/+internal/+gate/+gates

external/quantum/gate/@quantumCircuit

external/quantum/optimization

external/quantum/optimization/+quantum/+internal/+optimization

external/quantum/optimization/+quantum/+internal/+optimization/+tabusearch

external/quantum/optimization/+quantum/+internal/+optimization/+tabusearch/@MultiCallTabuSearch

external/quantum/optimization/@qaoa

external/quantum/optimization/@qaoaResult

external/quantum/optimization/@qubo

external/quantum/optimization/@quboResult

external/quantum/optimization/@tabuSearch

external/quantum/optimization/@tabuSearchResult

external/quantum/quantum/+quantum/+backend

external/quantum/quantum/+quantum/+internal

external/quantum/quantum/+quantum/+internal/+aws

external/quantum/quantum/+quantum/+internal/+ibm

external/quantum/quantum/+quantum/+internal/+transpile

external/tensor_toolbox

external/tensor_toolbox/@ktensor

external/tensor_toolbox/@tenmat

external/tensor_toolbox/@tensor

external/tensor_toolbox/@ttensor

external/tensor_toolbox/test

external/web_STRING/stringdb

private

doc

doc/mlx

Versions that use the GitHub default branch cannot be downloaded

Version Published Release Notes
25.9.0

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.9.0
25.8.9

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.9
25.8.8

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.8
25.8.7

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.7
25.8.6

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.6
25.8.5

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25.8.4

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.4
25.8.3

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.3
25.8.2

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.2
25.8.1

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.1
25.8.0

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.8.0
25.7.9

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.7.9
25.7.8

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.7.8
25.7.7

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.7.7
25.7.6

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.7.6
25.7.5

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25.7.4

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25.7.3

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25.7.2

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25.7.1

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25.7.0

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.7.0
25.6.1

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25.6.0

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25.5.2

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25.5.1

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25.5.0

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.5.0
25.4.9

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v25.4.9
25.4.8

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25.4.7

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25.4.6

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25.4.5

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25.4.4

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25.4.3

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25.4.2

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25.4.1

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25.3.9

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25.3.8

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25.3.7

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25.3.6

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25.3.5

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25.3.4

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25.3.3

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25.3.2

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25.3.1

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25.2.2

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25.2.1

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25.1.7

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25.1.6

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25.1.5

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25.1.4

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25.1.2

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25.1.1

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25.1.0

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24.9.0

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24.8.1

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24.8.0

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24.7.9

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24.7.8

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24.7.7

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24.7.6

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24.7.5

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24.7.3

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24.7.2

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24.7.1

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24.7.0

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24.6.9

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24.6.8

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24.6.7

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24.6.6

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24.6.5

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24.6.4

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24.6.3

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24.6.2

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24.6.1

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24.6.0

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24.5.9

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24.5.8

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24.5.7

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24.5.6

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24.5.5

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24.5.4

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24.5.3

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24.5.2

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24.5.1

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24.5.0

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24.4.9

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24.4.8

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24.4.7

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24.4.5

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24.4.4

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24.4.3

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24.4.2

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24.4.0

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24.3.9

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24.3.8

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24.3.7

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24.3.6

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24.3.5

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24.3.4

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24.3.3

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24.3.2

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24.3.1

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24.3.0

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24.2.0

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24.1.3

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24.1.1

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24.1.0

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23.9.0

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23.8.0

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23.7.0

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23.6.5.0

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23.6.0.0

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23.5.0.0

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23.4.7.0

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23.4.6

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23.4.5.0

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23.4.4.0

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23.4.2.0

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23.4.1

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23.3.2.0

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23.3.1.0

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23.3.0.0

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23.2.6.0

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23.2.4.0

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23.2.3.0

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23.2.1.0

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23.1.4.0

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23.1.3.0

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23.1.2.0

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23.1.1.0

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22.9.1

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22.7.1

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22.6.1

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22.4.11

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22.4.1

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22.3.6

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22.3.1

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22.2.21

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22.2.9

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22.1.31

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22.1.30

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22.1.29

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22.1.23

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22.1.19

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22.1.13

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21.12.28

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21.12.13

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21.12.10

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21.12.8

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21.12.04

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21.11.19

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21.11.18

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21.11.13

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21.11.6

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.11.6
21.10.17

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.10.17
21.9.30

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.9.30
21.9.23

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.9.23
21.9.7

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.9.7
21.9.3

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.9.3
21.9.2

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.9.2
21.8.29

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.8.29
21.8.24

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.8.24
21.8.9

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.8.9
21.8.4

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.8.4
21.8.1

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.8.1
21.7.29.0

See release notes for this release on GitHub: https://github.com/jamesjcai/scGEAToolbox/releases/tag/v21.7.29
21.7.26

new doc
21.7.14

new title
21.7.13

indicates the folder to be added when installing add-on
21.1.16

sc_scatter
21.1.15

SC_SCATTER(X, genelist)
21.1.14

Try new function: SC_SCATTER.m
Read documentation URL: https://scgeatoolbox.readthedocs.io/
20.8.2

add sc_celltypeexplorer_auto
20.7.5

cell marker gene identification function added.

1.0.0

To view or report issues in this GitHub add-on, visit the GitHub Repository.
To view or report issues in this GitHub add-on, visit the GitHub Repository.