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
☞ see Course tabFeatured Visualizations
Cell Type Exploration of Charmander Data Set
The cluster appears to be endothelial cells that make up adipose tissue. When looking at the Wilcox vs log2fc graph three of most significantly upregulated...
Identification of a Cluster Associated with CD8+ T cells
Description of my multi-panel plot Here, I identified a cluster that seems to be CD8+ T cells. In order to generate the plot above, I...
Homework 5
Description
Validation of cell type clustering via differential gene expression
The purpose of this visualization to present the usage of differential gene expression to validate cell type identification in k-means and tsne analysis of the...
Running tSNE analysis on genes or PCs
What data types are you visualizing? In this multi-panel plot, I am visualizing various quantitative and categorical data. For the PCA plot on the upper...
AQP1 Expression for Contrasting Principle Component Numbers
What data types are you visualizing? I am using categorical data (zero and nonzero expression) as well as quantitative (color gradient of expression).
Comparison of Dimensionality Reduction Methods for Representation of Clustered Data
What data are you visualizing
The effect of Count Per Million normalization on Dimensionality Reduction
What data types are you visualizing? I am visualizing quantitative data of cells’ position on tSNE embedded 2-dimensional space. I am also visualizing the total...
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...
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...
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,...
All Visualizations
Identification of the Breast Glandular Cells
The visualization presented above comprises eight panels, all of which provide evidence to support the hypothesis that cluster 1 corresponds to breast glandular cells, a type of epithelial cell (1)....
Validation of cell type clustering via differential gene expression
The purpose of this visualization to present the usage of differential gene expression to validate cell type identification in k-means and tsne analysis of the dataset. The quantitative data of...
Comparison of Dimensionality Reduction on Normal, Log10 Transformed and ScaleD Gene Expression
Should I normalize and/or transform the gene expression data (e.g. log and/or scale) prior to dimensionality reduction?
Effect of data transformation on linear dimensionality reduction
What data types are you visualizing?
Comparison of using normalized and unnormalized data on gene expression clustering in t-SNE graphs
What data types are you visualizing? I am visualizing quantitative data of the comparative gene expression of two genes KRT7 and PTPRC. I am also visualizing the quantitative data of...
Effects of normalizing by gene count in the reduced dimension visualization
What data types are you visualizing? I present quantitative data of the PCA and tSNE reduced dimension applied to the raw gene expression data and the normalized by gene count...
The effects of log transformation, scaling and normalization prior to PCA and non-linear dimensionality reduction (tSNE) on PDGFRB gene expression data
What data types are you visualizing? I am visualizing quantitative data of 2 dimensional reduction through PCA and tSNE of original PDGFRB expression for each cell, quantitative data of 2...
Dimensionality Reduction approach for spatial transcriptomics in genes ZEB1 and ZEB2
1. Should I normalize and/or transform the gene expression data (e.g. log and/or scale) prior to dimensionality reduction? It is recommended to normalize the data with scale to help take...
Clusters of Genes Expressing ERBB2 using t-SNE
What data types are you visualizing? I am visualizing the similarities in levels of overall gene expression in cells that have non-zero expression of ERBB2 and the level of expression...
Running tSNE analysis on genes or PCs
What data types are you visualizing? In this multi-panel plot, I am visualizing various quantitative and categorical data. For the PCA plot on the upper left, I am visualizing quantitative...
AQP1 Expression for Contrasting Principle Component Numbers
What data types are you visualizing? I am using categorical data (zero and nonzero expression) as well as quantitative (color gradient of expression).
