Welcome

Welcome to the Course Website for EN.580.428 Genomic Data Visualization!

As the primary mode through which analysts and audience members alike consume data, data visualization remains an important hypothesis generating and analytical technique in data-driven research to facilitate new discoveries. However, if done poorly, data visualization can also mislead, bias, and slow down progress. This hands-on course will cover the principles of perception and cognition relevant for data visualization and apply these principles to genomic data, including large-scale single-cell and spatially-resolved omics datasets, using the R statistical programming language. Students will be expected to complete class readings, create weekly data visualizations as homework assignments, and make a major class presentation.

Course Information

Course Staff: Prof. Jean Fan and Kalen Clifton
Office Hours: 10:00am-10:50am Monday, Wednesday, and Friday. See Slack for location details.
Lectures: 8:00am-9:50am Monday, Wednesday, and Friday. See Slack for location details.

Course Details
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All Visualizations

Spatial Expression of the 3 Most Significantly Expressed Genes in All Cells

What data types are you visualizing? I am visualizing quantitative data of the expression level of the three most significantly expressed genes across all cells for each cell, quantitative data...

Relationship between cells' spatial position and GATA3 expression

What data types are you visualizing? In this plot, I am visualizing quantitative data of each cell’s expression count of the GATA3 gene and quantitative data of each cell’s spatial...

The Spatially Variant Expression Pattern of AGR3

What data types are you visualizing?

Cells Clustered By Gene Expression

What data are you visualizing

Comparative detection of KRT7 and PTPRC gene expression

What data types are you visualizing? I am visualizing categorical data of the comparative gene expression detection of two genes KRT7 and PTPRC. There are four possible categories: only KRT7...

Expression level of the most variable gene ERBB2 in TSNE plot

What data types are you visualizing? I am visualizing quantitative data of the expression count of the most variable gene ERBB2 for each cell, and spatial data regarding the x,y...

Spatial position of cells with low gene count

What data types are you visualizing? I am visualizing the categorical data of the presence of 3 or fewer genes in a cell together with the spatial data of the...

Comparing the relationship between Growth Factor Receptors Expression and Cell Area

What data types are you visualizing? I am visualizing quantitative data of the expression count of the EGFR, PDGFRA and PDGFRB genes for each cell, quantitative data of the area...

Relationship between Number of Genes Expressed and Cell Area

What data types are you visualizing? I am visualizing the given quantitative data type of “Cell Area”, and the calculated quantitative data type of “Number of Genes Expressed” (calculated by...

Homework 1 Submission

What data types are you visualizing?

Relationship between ERBB2 Expression and Cell Area

What data types are you visualizing? I am visualizing quantitative data of the expression count of the ERBB2 gene for each cell, quantitative data of the area for each cell,...