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scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Home Page: https://www.mathworks.com/matlabcentral/fileexchange/72917-scgeatoolbox-single-cell-gene-expression-analysis-toolbox

License: MIT License

MATLAB 32.10% M 0.02% HTML 67.84% C 0.03% Objective-C 0.01%

scrna-seq workflow demo-scripts analyses dimensionality trajectory matlab-toolbox rna-seq-analysis tsne phate

scgeatoolbox's Issues

Use primme_svds in sc_pcnet

https://github.com/primme/primme

add c-CSN

https://github.com/LinLi-0909/c-CSN

F-T transformation

https://github.com/flo-compbio/monet/blob/master/monet/util/expression.py

improve the pseudotime gene expression curve viewer

cell-cycle-prediction

https://oscar-franzen.github.io/adobo/#cell-cycle-prediction

Adding Scedar

add NFE

https://www.sciencedirect.com/science/article/pii/S1672022921000589#b0315

add Louvain

https://github.com/GenLouvain/GenLouvain

adding function for cell subtype annotation

Adding Harmony (level 1)

Adding douplet detection

https://github.com/JonathanShor/DoubletDetection

https://github.com/AllonKleinLab/scrublet

Missing demo data file

Hi James,

This is a great tool! I tried to run the demos. One data file is missing for the following demos:
Demo 2, line 2: [X,genelist] =sc_readfile('example_data/GSM3044891_GeneExp.UMIs.10X1.txt');
Demo 3: line 4: [Z,genelistz]=sc_readfile('example_data/GSM3044891_GeneExp.UMIs.10X1.txt');
Demo 5: line 2: [X,genelist] =sc_readfile('example_data/GSM3044891_GeneExp.UMIs.10X1.txt');
Can you please add the data file? Thanks.

Gang Wu

add gtsne

mergesce error when sce1.c and sce2.c are different data type

Adding scibet (level 1)

https://github.com/PaulingLiu/scibet

gui.i_exporttable

gui.i_exporttable

adding slingshot

https://github.com/oscar-franzen/adobo/blob/master/adobo/traj.py

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