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Course10210555642 lectures

Biological data analysis and visualization with R

Prof. Riddhiman Dhar · IIT Kharagpur

Start with lecture 1 At NPTEL

Lectures

week-01

  1. Lecture 01 : Introduction Video
  2. Lecture 02 : Setting up R Video
  3. Lecture 03 : Basic functions in R Video
  4. Lecture 04 : Basic data structures in R Video
  5. Lecture 05 : Data structures and File I/O Video

week-02

  1. Lecture 06 : Basic statistical tests with R Video
  2. Lecture 07 : Correlation analysis Video
  3. Lecture 08 : Analysis of variance (ANOVA) Video
  4. Lecture 09 : Basic data visualization techniques Video
  5. Lecture 10 : Data visualization Video

Week 3 :

  1. Lecture 11 : Visualization with vioplot and ggplot2 Video
  2. Lecture 12 : R packages for plotting and data organization Video
  3. Lecture 13 : Data transformation in R Video
  4. Lecture 14 : Bioconductor packages Video
  5. Lecture 15 : Flow cytometry data analysis in R/Bioconductor Video

Week 4 :

  1. Lecture 16 : Gene expression analysis and co-expression network Video
  2. Lecture 17 : WGCNA package and Data Download Video
  3. Lecture 18 : WGCNA hands-on: Data preprocessing Video
  4. Lecture 19 : WGCNA hands-on: Soft-threshold Video
  5. Lecture 20 : WGCNA: Module gene expression Video

Week 5 :

  1. Lecture 21 : Introduction to ChIP-seq Video
  2. Lecture 22 : ChIP-seq data analysis Video
  3. Lecture 23 : ChIP-seq data analysis: Peak calling Video
  4. Lecture 24 : Peak calling and Visualization Video
  5. Lecture 25 : ChIP-seq data analysis: bigWig/bw files Video

Week 6 :

  1. Lecture 26 : Regression models on Biological data Video
  2. Lecture 27 : Predictive models with linear regression Video
  3. Lecture 28 : Multicollinearity Video
  4. Lecture 29 : Lasso regression Video
  5. Lecture 30 : Non-linear regression Video

Week 7 :

  1. Lecture 31: Dimensionality reduction Video
  2. Lecture 32 : Principal Component Analysis (PCA) Video
  3. Lecture 33: PCA analysis hands-on Video
  4. Lecture 34: PCA analysis using ‘PCAtools’ Video
  5. Lecture 35 : UMAP analysis Video

Week 8 :

  1. Lecture 36 : Classification of biological samples Video
  2. Lecture 37 : Penalized and Stepwise Logistic regression Video
  3. Lecture 38 : Decision trees Video
  4. Lecture 39 : Classification and Regression trees Video
  5. Lecture 40 : Random Forests Video

Live Session

  1. Live Session 10-03-2025 Video
  2. Live Session 16-04-2025 Video

Syllabus and materials

At NPTEL, as the course publishes them.

Credits and licence

Institution
IIT Kharagpur
Department
Biotechnology
Teacher
Prof. Riddhiman Dhar
Level
Undergraduate
Language
English
Subjects
Biology
Source
NPTEL
Licence
CC BY-NC-SA, as NPTEL states it. Non-commercial use only. NPTEL's terms
Attribution
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