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scGEAToolbox

version 1.0.0 (123 MB) by James Cai
a Matlab toolbox for single-cell RNA-seq data analyses

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Updated 01 Oct 2019

GitHub view license on GitHub

Single-cell RNA sequencing (scRNA-seq) technology has revolutionized the way research is done in biomedical sciences. It provides an unprecedented level of resolution across individual cells for studying cell heterogeneity and gene expression variability. Analyzing scRNA-seq data is challenging though, due to the sparsity and high dimensionality of the data. I developed scGEAToolbox—a Matlab toolbox for scRNA-seq data analysis. It contains a comprehensive set of functions for data normalization, feature selection, batch correction, imputation, cell clustering, trajectory/pseudotime analysis, and network construction, which can be combined and integrated to building custom workflow. While most of the functions are implemented in native Matlab, wrapper functions are provided to allow users to call the “third-party” tools developed in Matlab or other languages. Furthermore, scGEAToolbox is equipped with sophisticated graphical user interfaces (GUIs) generated with App Designer, making it an easy-to-use application for quick data processing

Cite As

James Cai (2019). scGEAToolbox (https://www.github.com/jamesjcai/scGEAToolbox), GitHub. Retrieved .

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MATLAB Release Compatibility
Created with R2019a
Compatible with any release
Platform Compatibility
Windows macOS Linux
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thirdparty/CSN_transform

thirdparty/ClusterPack

thirdparty/ComBat

thirdparty/DensityClust

thirdparty/DensityClust/cluster_dp

thirdparty/DensityClust/density_clust_test

thirdparty/FIt-SNE

thirdparty/GENIE3

thirdparty/GENIE3/RT

thirdparty/GSEA

thirdparty/HCI_high_order_corr_integ

thirdparty/HCI_high_order_corr_integ/PFA_pattern_fusion_analysis

thirdparty/HCP_hidden_covariates_with_prior

thirdparty/MAGIC

thirdparty/McImpute

thirdparty/Network_Enhancement

thirdparty/Network_Enhancement/core

thirdparty/Network_Enhancement/examples/Butterfly_Network

thirdparty/Network_Enhancement/examples/HiC_Network

thirdparty/PHATE

thirdparty/R_monocle

thirdparty/SIMLR

thirdparty/SIMLR/src

thirdparty/SinNLRR

thirdparty/SoptSC

thirdparty/SoptSC/NNDSVD

thirdparty/SoptSC/symnmf2

thirdparty/SoptSC/vinlinplot

thirdparty/bigSCale

thirdparty/diffusion_map_annlee

thirdparty/difussion_map_icb

thirdparty/faster_svd/lmsvd

thirdparty/faster_svd/svdandpca

thirdparty/locfit/Book

thirdparty/locfit/Neuro

thirdparty/locfit/Source

thirdparty/locfit/m