NYRaMP-Informatics-2024: Difference between revisions

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<center>'''BioMedical Genomics'''</center>
<center>'''NYRaMP Informatics Workshop'''</center>
<center>August 2024, Tuesdays 10-12 noon, DNA Learning Center</center>
<center>August 2024, Tuesdays 10-12 noon, DNA Learning Center</center>
<center>'''Instructor:''' Weigang Qiu, Ph.D., Professor, Department of Biological Sciences, Hunter College, CUNY; '''Email:''' wqiu@.hunter.cuny.edu</center>
<center>'''Instructor:''' Weigang Qiu, Ph.D., Professor, Department of Biological Sciences, Hunter College, CUNY; '''Email:''' wqiu@.hunter.cuny.edu</center>
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==Learning goals==
==Learning goals==
By the end of this course successful students will be able to:  
By the end of this workshop students will be able to:  
* Describe next-generation sequencing  (NGS) technologies & contrast it with traditional Sanger sequencing
* Visualize genomics data using R & RStudio
* Explain applications of NGS technology including pathogen genomics, cancer genomics, human genomic variation, transcriptomics, meta-genomics, epi-genomics, and microbiome.
* Perform t-tests, regression analysis, and association tests with R & Rstudio
* Visualize and explore genomics data using R & RStudio
* Interpret results of data visualization & statistical analysis
* Replicate key results using a raw data set produced by a primary research paper
 
==Web Links==
==Web Links==
* Install R base: https://cloud.r-project.org
* Install R base: https://cloud.r-project.org

Revision as of 15:25, 1 August 2024

NYRaMP Informatics Workshop
August 2024, Tuesdays 10-12 noon, DNA Learning Center
Instructor: Weigang Qiu, Ph.D., Professor, Department of Biological Sciences, Hunter College, CUNY; Email: wqiu@.hunter.cuny.edu
T.A.: Brandon Ely, CUNY Graduate Center; Email:bely@gradcenter.cuny.edu
MA plot Volcano plot Heat map
fold change (y-axis) vs. total expression levels (x-axis)
p-value (y-axis) vs. fold change (x-axis)
genes significantly down or up-regulated (at p<1e-4)

Overview

A genome is the total genetic content of an organism. Driven by breakthroughs such as the decoding of the first human genome and rapid DNA and RNA-sequencing technologies, biomedical sciences are undergoing a rapid & irreversible transformation into a highly data-intensive field, that requires familiarity with concepts in both biological, computational, and statistical sciences.

Genome information is revolutionizing virtually all aspects of life sciences including basic research, medicine, and agriculture. Meanwhile, use of genomic data requires life scientists to be familiar with concepts and skills in biology, computer science, as well as statistics.

This workshop is designed to introduce computational analysis of genomic data through hands-on computational exercises.

Learning goals

By the end of this workshop students will be able to:

  • Visualize genomics data using R & RStudio
  • Perform t-tests, regression analysis, and association tests with R & Rstudio
  • Interpret results of data visualization & statistical analysis

Web Links

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