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1
Intro
2
WGCNA Workflow steps at a glance
3
Study Design
4
Fetch Data and read data in R
5
Get metadata using GEOquery package
6
Manipulate expression data
7
Quality Control - Remove outlier samples and genes; using goodSampleGenes
8
Detecting outliers using hierarchical clustering
9
Detecting outliers using Principal Component Analysis PCA
10
Data Normalization using vst from DESeq2 package
11
filtering out genes with low counts
12
Pick soft threshold
13
Identify Modules
14
maxBlockSize parameter
15
Get module eigengenes
16
Visualize modules as dendrogram
Description:
Embark on a comprehensive step-by-step tutorial exploring Weighted Gene Co-expression Network Analysis (WGCNA) using RNA-Seq data. Learn data manipulation techniques, outlier detection methods for genes and samples, normalization procedures, soft threshold selection, module identification, and dendrogram visualization. Follow along as the instructor demonstrates each step using R, covering topics such as data retrieval, metadata extraction with GEOquery, quality control measures, hierarchical clustering, Principal Component Analysis (PCA), data normalization with DESeq2, gene filtering, and module eigengene calculation. Gain practical insights into WGCNA workflow and its application in analyzing gene co-expression networks.

Weighted Gene Co-expression Network Analysis - Step-by-Step Tutorial - Part 1

Bioinformagician
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