Applied Bioinformatics BIOL441 Fall 2024 (4 credit) (5 students) *Graduate Class (Masters & Ph.D. Level): https://www.claflin.edu/ Claflin University, Orangeburg, South Carolina, USA. https://www.claflin.edu/academics-research/schools-departments/school-of-natural-sciences-and-mathematics/department-of-mathematics-computer-science/computer-science
January 9 2023.
This is the class content for BIOL441. The GitHub link is Here
Bioinformatics:
Phylogenetic Analysis: https://youtu.be/IMIP4la-K84
Github: https://github.com/spawar2/BTEC-620-Spring-2023
Bioinformatics (topics including sequence alignment algorithms, scoring matrices, microarray analysis, phylogenetic analysis, bootstrapping, tree building, secondary & tertiary structure prediction, homology modeling, and protein folding)], visualization: heat maps, volcano plots, pie charts, Blast, Sequence alignments (Margaret Dayhoff, PAM, blossom scoring matrices, global & local alignment).Gene Expression Omnibus (GEO) datasets mining, Microarray data analysis: Read, Pre-processing/Normalization (Affy, Oligo, Limma-RMA, Quantile, Mas5.0), Visualization: Heat maps, box plots, Fold change expression analysis, Gene Set Enrichment Analysis (GSEA), Pathways and protein downstream interactome analysis.
Sequence alignments (Margaret Dayhoff, PAM, Blossom scoring matrices, global & local alignment): https://youtu.be/Lx1jkr3UKwA
Print statement: https://campuspress.yale.edu/shrikantpawar/files/2024/08/Screenshot-2024-08-19-at-9.51.47%E2%80%AFAM-300x61.png
Set working directory: https://campuspress.yale.edu/shrikantpawar/files/2024/08/Correlatin-300x187.png
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Affy-Read-300x134.png
Raw microarray plot: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Raw-data.pdf
Box plot code: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Screenshot-2024-09-06-at-9.49.11%E2%80%AFAM-300x191.png
Robust Multiarray Normalized (RMA) plot: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Nomalized-Plot.pdf
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Program-300x207.pnghttps://campuspress.yale.edu/shrikantpawar/files/2024/09/Screenshot-2024-09-11-at-9.45.39%E2%80%AFAM-300x178.png
Fold Change Analysis: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Fold-Change-Analysis-Microarray-300x214.png
Phylogenetic-Analysis: https://campuspress.yale.edu/shrikantpawar/files/2024/09/Phylogenetic-Analysis-300x142.png
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Phylogenetic-Analysis-1-300x206.png
https://campuspress.yale.edu/shrikantpawar/files/2024/09/Phylogenetic-tree.pdf
All Videos
All Videos
WorldS4 2023
Madhuhas-Stanford-Testimonial
K-Fold Semi-Supervised-Video
