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institute of biotechnology
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bioinformatics
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workshops
Workshops
Single-cell RNAseq Analysis Virtual Workshop
Click here to register for this workshop
Hands-on computer assignment.
This workshop is jointly hosted by the Bioinformatics Facility and Genomics Facility of Cornell Institute of Biotechnology. It will cover basic skills to analyze single-cell RNAseq data. Participants can take the 4-session workshop at your own pace. Each session includes one recorded video, and a set of data analysis projects on a provided Linux server. You can sign up for office hours
at this web site
.
Pre-requisites:
Basic Linux command line and R skills are required to take this workshop. If you are not familiar with Linux operating system, you can take
this beginners' workshop
, or the more extensive
three-session Linux workshop
. During this SC RNAseq workshop, we will provide step-by-step instructions how to finish the projects, and some guidance how to do Linux and R. Python package Scanpy will be introduced in the 4th session. Python coding skill is not required during the workshop, but you will need to develop Python skill in order to analyze your own data using Scanpy.
Syllabus:
Session 1. Single cell technology, from samples to raw data to count matrix
• Intro to single-cell technologies, including e
xperimental design and expectations;
• Using 10x cellranger count for gene expression;
• Using 10x Loupe browser for exploration of results;
Recorded sessions:
video 1
Session 2,3. Biological data analysis in Seurat part 1 and part 2
• Data structure, filtering and basic QC;
• Sample n
ormalization, i
ntegration and clustering;
• Markers for cell type identification;
• Comparative analysis between populations of cells;
• Gene set analysis;
• Visualization;
Recorded sessions:
video 2
video 3
Session 4. Beyond Seurat
• Intro to scanpy;
• Batch effect in data integration;
• Imputation;
• Trajectory analysis;
Recorded sessions:
video 4
Server assignment length 14 days
Session 1
Jan 1 1900 12:00AM - 12:00AM
Single cell technology, from samples to raw data to count matrix.
Download
:
slides
,
hands-on
Video:
video 1
Session 2
Jan 1 1900 12:00AM - 12:00AM
Biological data analysis - part 1
Download
:
slides
,
hands-on
Video:
video 2
Session 3
Jan 1 1900 12:00AM - 12:00AM
Biological data analysis - part 2
Download
:
slides
,
hands-on
Video:
video 3
Session 4
Jan 1 1900 12:00AM - 12:00AM
Beyond Seurat
Download
:
slides
,
hands-on
Video:
video 4
Session 5
Mar 6 2024 12:00PM - 12:00PM
Extra hands on:
From Seurat to Loupe
Exporting Seurat to SingleCellExperiment object
Website credentials:
login
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