Transcriptome Data Analysis Using DESeq
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Overview

​Objective of this course is to introduce you the general practice for transcriptome data analysis using advanced statistical models. We will use DEseq, a Bioconductor package.

Course content

Introduction
  • R, Rstudio, Bioconductor
  • RNASeq
    • Experimental design
    • Application
    • File formats (FastQ, BAM, Count, GTF, BED)
  • RNASeq data analysis workflow
    • Alignment based (Tophat, Hisat, etc)
    • Non-alignment based (Kallisto, RSEM, Htseq-count)
Dataset
  • Understand the dataset to be used in this course

Exploratory data analysis
  • Data filtering
    • Gene filtering based on no/low expression values
  • Data transformation
    • rLog transformation
    • Variance stabilizing transformations (VST transformation)
  • Measure of dissimilarity between conditions
    • Euclidean distance based
    • Poisson Distance (PoiClaClu package)
Data Visualization
  • Distance matrix heatmap
  • Visualize sample-to-sample distance via Multi dimensional scaling (MDS)
  • Visualize sample-to-sample distance via Principal component analysis (PCA)
Differential gene expression
  • Gene wise differential expression using DESeq package
  • Understand experimental design
  • Data normalization
  • Effect size estimate
  • Design contrast
  • False discovery rate estimation
  • Concept of Multiple testing correction
  • Surrogate variable analysis
Visualization of results
  • Counts plots
  • MA plot
  • Gene clustering
Annotation
  • Annotation through AnnotationDbi and org.Hs.eg.db package
Genomic space plotting (Gviz package)

Reporting the results (ReportingTools package)

Highlights

  • Learn various data transformation methods
  • Learn various normalization methods for count data

Duration

  • Online training.
  • 15-20 hr
  • Flexible timings as per your conveniences.

Extra Benefits

  • Course certificate will be provided
  • Course materials will be provided
  • Post training, if you need any help in writing codes for solving any of your research problem, assistance and guidance will be provided.

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