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Computational Approaches for Omics

CAfO

Biomedical Omics — University of Milan "La Statale". Lessons, exercises, solutions and datasets for the R-based computational omics course.

01 — Lessons
01Installation of R and RStudio 02Introduction to R 03R basics — Data types 04R basics — Input / Output 05Functions & control structures 06R Markdown 07R basics — Plot 08Graphics — ggplot2 09Bioconductor 10Data scaling 11Dimensionality reduction 12Principles of statistics 13RNA structure 14Distance, clustering & heatmaps 15Heatmaps 16DESeq2 & ORA — Tutorial 17DESeq2 & ORA
02 — Exercises
01Operations and vectors 02Vectors 03Matrices 04Lists and Data frames 05Input / Output 06Functions, if/else, for, while 07Basic plot 08Plot from DF, colors, margins 09ggplot2 10PCA & heatmap 11Clustering · Heatmap 12DESeq2 & ORA 13scRNA-seq analysis 14ML for Cancer Classification 15ML exercise — PRAD vs LUAD
03 — Solutions
01Operations and vectors 02Vectors 03Matrices 04Lists and Data frames 05Input / Output 06Functions, if/else, for, while 07Basic plot 08Plot from DF, colors, margins 09ggplot2
04 — Datasets
01vcap_foxa1_expression.csv 02vcap_foxa1_metadata.csv 03FOXA1_PC3_exprs.rds 04TCGA_COAD_TPM.rds 05TCGA_COAD_metadata.rds