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1
Introduction and background
2
Chapter 1 - Installing packages and importing libraries
3
Using TCGA Biolinks
4
Structuring Input data and filtering
5
PlotMDS from limma and edgeR
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Normalization of data
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PCA Analysis
8
Making Train Label and One -hot Encoding
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Chapter 2 - Neural network construction
10
Neural networking Training model fitting
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Saving Model as hdf5 files
12
Extraction weights and bias
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Extraction of GOI using weights and bias
14
Chapter 3 - Gene set enrichment analysis
15
Results!!!!!!
16
Some major issues with this approach
Description:
Explore a comprehensive 50-minute tutorial on identifying TCGA biomarkers using machine learning techniques. Learn to install necessary packages, import libraries, and utilize TCGA Biolinks for data retrieval. Discover methods for structuring and filtering input data, performing normalization, and conducting PCA analysis. Dive into neural network construction, model training, and saving models as HDF5 files. Extract weights, biases, and genes of interest from the trained model. Conduct gene set enrichment analysis and interpret results. Gain insights into potential limitations of this approach while following along with provided slides and scripts. Perfect for those interested in bioinformatics and machine learning applications in cancer research.

TCGA Biomarkers Identification Using Machine Learning - Complete Walkthrough

LiquidBrain Bioinformatics
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