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scGEAToolbox (single-cell Gene Expression Analysis Toolbox)

version 21.10.17 (26.6 MB) by James Cai
Single-cell Gene Expression Analysis Toolbox

330 Downloads

Updated 18 Oct 2021

From GitHub

View license on GitHub

scGEAToolbox - a Matlab toolbox for single-cell RNA-seq data analyses

Introduction

Motivation: 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.
Results: 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.
Availability: https://github.com/jamesjcai/scGEAToolbox

View scGEAToolbox on File Exchange

Contact: jcai@tamu.edu

Install in MATLAB:

disp('Install scGEAToolbox...')
unzip('https://github.com/jamesjcai/scGEAToolbox/archive/master.zip');
addpath('./scGEAToolbox-master');

Read Documentation

scGEAToolbox Documentation

Help

If you have any questions or require assistance using scGEAToolbox, please contact me at scgeatoolbox.slack.com

Citation

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

MATLAB Release Compatibility
Created with R2021a
Compatible with any release
Platform Compatibility
Windows macOS Linux

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+gui

+gui/private

+pkg

+run

+run/private

+run/thirdparty/CSN_transform

+run/thirdparty/ClusterPack

+run/thirdparty/ComBat

+run/thirdparty/GENIE3

+run/thirdparty/GENIE3/RT

+run/thirdparty/HCP_hidden_covariates_with_prior

+run/thirdparty/MAGIC

+run/thirdparty/MPPC

+run/thirdparty/McImpute

+run/thirdparty/Network_Enhancement

+run/thirdparty/Network_Enhancement/core

+run/thirdparty/PHATE

+run/thirdparty/R_UCell

+run/thirdparty/R_monocle

+run/thirdparty/SIMLR

+run/thirdparty/SIMLR/src

+run/thirdparty/SNNDPC

+run/thirdparty/SinNLRR

+run/thirdparty/SoptSC

+run/thirdparty/SoptSC/NNDSVD

+run/thirdparty/SoptSC/symnmf2

+run/thirdparty/SoptSC/vinlinplot

+run/thirdparty/Specter

+run/thirdparty/Specter/LSC

+run/thirdparty/Specter/dimred

+run/thirdparty/Specter/utils

+run/thirdparty/TSEE

+run/thirdparty/alona_panglaodb

+run/thirdparty/alona_panglaodb/brain

+run/thirdparty/alona_panglaodb/heart

+run/thirdparty/alona_panglaodb/immunesystem

+run/thirdparty/alona_panglaodb/pancreas

+run/thirdparty/alona_panglaodb/thymus

+run/thirdparty/alona_panglaodb2021

+run/thirdparty/cbrewer

+run/thirdparty/celltype_mat_new

+run/thirdparty/faster_svd/lmsvd

+run/thirdparty/faster_svd/svdandpca

+run/thirdparty/k-NN-code

+run/thirdparty/locfit/Neuro

+run/thirdparty/locfit/Source

+run/thirdparty/locfit/m

+run/thirdparty/py_harmonypy

+run/thirdparty/py_harmonypy/old

+run/thirdparty/umapFileExchange/umap

+run/thirdparty/umapFileExchange/util

+ten

@SingleCellExperiment

@SingleCellNetwork

private

resources

resources/STRING

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.