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Meta-SVM/RFE-Permutation joint method for identification of DEGs

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Chunk01-R script for gene expression data simulation based on improved compcodeR.R
Chunk01-R script for gene expression data simulation based on improved compcodeR.R
 
 
Chunk02-Data simulation of transcriptome including microarray and RNA-seq datasets.R
Chunk02-Data simulation of transcriptome including microarray and RNA-seq datasets.R
 
 
Chunk03-Preparing the sub-groups from primary DNA microarray or RNA-seq dataset.R
Chunk03-Preparing the sub-groups from primary DNA microarray or RNA-seq dataset.R
 
 
Chunk04-Robust biomarker selection based on meta-analysis.R
Chunk04-Robust biomarker selection based on meta-analysis.R
 
 
Chunk05-Gene selection based on SVM-RFE approach.R
Chunk05-Gene selection based on SVM-RFE approach.R
 
 
Chunk06-Gene selection based on permutation test.R
Chunk06-Gene selection based on permutation test.R
 
 
Chunk07-MSP method to identify the potential biomarkers and performance evaluation.R
Chunk07-MSP method to identify the potential biomarkers and performance evaluation.R
 
 
Chunk08-Ten classic gene selection methods used in this study.R
Chunk08-Ten classic gene selection methods used in this study.R
 
 
Chunk09-Comprehensive comparison and evaluation for MSPJ and others.R
Chunk09-Comprehensive comparison and evaluation for MSPJ and others.R
 
 
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LICENSE
 
 
README.md
README.md
 
 

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MSPJ

MSPJ GPLv3 license

MSPJ: discovering potential biomarkers in small gene expression datasets via ensemble learning

  • Huachun Yin, Jingxin Tao, Bo Li, et al.

Please Cite: HuaChun Yin, JingXin Tao, Yuyang Peng, Ying Xiong, Bo Li, Song Li, Hui Yang. MSPJ: discovering potential biomarkers in small gene expression datasets via ensemble learning. Computational and Structural Biotechnology Journal, 2022, DOI:10.1016/j.csbj.2022.07.022

PS: All artificial datasets used to evaluate the performance of gene selection methods were deposited in the Zenodo repository DOI:10.5281/zenodo.6320499. The real datasets were collected from GEO and pre-processed according to the pipeline described in this manuscript.

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Meta-SVM/RFE-Permutation joint method for identification of DEGs

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