Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center...
Transcript of Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center...
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Harvard Chan Bioinformatics Core
https://hbctraining.github.io/Intro-to-R-with-DGE/
Introduction to R and Differential Expression Analysis
![Page 2: Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center for Stem Cell Bioinformatics Harvard Catalyst Bioinformatics Consulting HMS Tools](https://reader030.fdocuments.net/reader030/viewer/2022040110/5d5f708b88c993a77b8bccd5/html5/thumbnails/2.jpg)
Harvard Chan Bioinformatics Core
Mary Piper
John Hutchinson
Lorena Pantano
Brad Chapman
Peter Kraft
Rory Kirchner
Meeta Mistry Radhika Khetani
Shannan Ho Sui
Victor BarreraMichael Steinbaugh Kayleigh Rutherford
![Page 3: Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center for Stem Cell Bioinformatics Harvard Catalyst Bioinformatics Consulting HMS Tools](https://reader030.fdocuments.net/reader030/viewer/2022040110/5d5f708b88c993a77b8bccd5/html5/thumbnails/3.jpg)
Consulting
• RNA-seq, small RNA-seq and ChIP-seq analysis
• Genome-wide methylation
• WGS, resequencing, exome-seq and CNV studies
• Quality assurance and analysis of gene expression arrays
• Functional enrichment analysis
• Grant support
http://bioinformatics.sph.harvard.edu/
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Training
• Short workshops on introductory, intermediate and
advanced topics related to NGS data analysis
• In-depth course - September 5th -October 11th
http://tinyurl.com/ngs-course-info-2018
• Monthly, 2-3 hour, hands-on and free workshops on “Current Topics in Bioinformatics”
http://bioinformatics.sph.harvard.edu/training/#upcoming-workshopscourses
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NIEHS / CFAR Bioinformatics
Core
Center for Stem Cell
Bioinformatics
Harvard Catalyst
Bioinformatics Consulting
HMS Tools &
Technology
![Page 6: Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center for Stem Cell Bioinformatics Harvard Catalyst Bioinformatics Consulting HMS Tools](https://reader030.fdocuments.net/reader030/viewer/2022040110/5d5f708b88c993a77b8bccd5/html5/thumbnails/6.jpg)
NIEHS / CFAR Bioinformatics
Core
Center for Stem Cell
Bioinformatics
Harvard Catalyst
Bioinformatics Consulting
HMS Tools &
Technology
![Page 7: Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center for Stem Cell Bioinformatics Harvard Catalyst Bioinformatics Consulting HMS Tools](https://reader030.fdocuments.net/reader030/viewer/2022040110/5d5f708b88c993a77b8bccd5/html5/thumbnails/7.jpg)
Introductions!
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Harvard Chan Bioinformatics Core
Mary Piper
John Hutchinson
Lorena Pantano
Brad Chapman
Peter Kraft
Rory Kirchner
Meeta Mistry Radhika Khetani
Shannan Ho Sui
Victor BarreraMichael Steinbaugh Kayleigh Rutherford
![Page 9: Introduction to R and Differential Expression Analysis · Training • Short workshops ... Center for Stem Cell Bioinformatics Harvard Catalyst Bioinformatics Consulting HMS Tools](https://reader030.fdocuments.net/reader030/viewer/2022040110/5d5f708b88c993a77b8bccd5/html5/thumbnails/9.jpg)
Class Introductions!
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Workshop Scope…
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http://anoved.net/tag/lego/page/3/
Learning R
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Learning objectives
Workshop Scope (1/2)
R basics ✓ Become comfortable with RStudio (a graphical interface for R)
✓ Fluently interact with R using RStudio
✓ Become familiar with R syntax
✓ Understand data structures in R
✓ Inspect and manipulate data structures
✓ Install packages and use functions in R
✓ Visualize data using simple and complex plotting methods
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Learning objectives
Differential Gene Expression analysis ✓ Understand the considerations for performing statistical analysis on RNA-
seq data
✓ Start with gene counts (after alignment and counting)
✓ Perform QC on count data
✓ Use DESeq2 to perform differential expression analysis on the count data and obtain a list of significantly different genes
✓ Visualization of differentially expressed genes
Workshop Scope (2/2)
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Contact us!
HBC training team: [email protected]
HBC consulting: [email protected]
@bioinfocoreTwitter