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session1a.Rmd
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---
title: "Introduction to Cytoscape and it's Apps - Session 1a"
author: "Akshay Bhat"
date: '`r format(Sys.time(), "Last modified: %d %b %Y")`'
output:
html_notebook:
toc: yes
toc_float: yes
css: stylesheets/styles.css
pdf_document:
toc: yes
---
<img src="images/logo-sm.png" style="position:absolute;top:40px;right:10px;" width="200" />
# Part A: Network Analysis with Cytoscape
## Goals and Motivations
By the end of these sessions you should be able to:
* Understand the major applications of network biology
* Find relevant networks and pathways
* Import your data into Cytoscape
* Perform basic topological and other network analyses
* Master network layouts and data visualization
* Know where to find relevant Cytoscape apps and tutorials
* Be able to analyze RNA-seq data using Cytoscape.
# Introduction to Network Biology
## **Why Networks?**
**Networks are everywhere...** especially in biology!
* Molecular networks
* Understand the major applications of network biology
* Find relevant networks and pathways
* Cell-cell communication
* Nervous systems
* Social networks
## **Transcriptomics**
* In the early days:
* Then came microarrays:
* And now, the network view:
## **Single Cell Transcriptomics**
## **Proteomics**
## **Networks are powerful tools...**
* Reduce complexity
* More efficient than tables
* Great for data integration
* Intuitive visualization
## Advantages of Networks as Tool
**Analysis**
* Topological properties
* Hubs and subnetworks
* Classify, cluster and diffuse
* Data integration
**Visualization**
* Data overlays
* Layouts and animation
* Exploratory analysis
* Context and interpretation
## Applications in Research
([Click Here for more network examples:](https://www.ncbi.nlm.nih.gov/pmc/?term=(cytoscape+AND+network)+AND+(%222022/01/01%22[PUBDATE]+%3A+%223000/01/01%22[PUBDATE])&report=imagesdocsum&dispmax=100))
# Biological Network Taxonomy
## Pathways
* Metabolic
* Signaling
* Regulatory
* Disease
## Interactions
## Similarity
<br></br>
### We will now go to the next [session (1 B)](session1b.nb.html) to understand terms about public repositories.