Introduction

This repository contains Biplots, Volcano plots, PCA plots, Heatmaps and more Computational Genomics data created and visualized during the University of Pittsburgh course, Computational Biology (BIOSC1540), with Dr. Miler Lee.

Note: The following visualizations were created using a combination of Bash and R

Files

📄 Miscellaneous Visualizations/ Assorted Visualizations.pdf

Contains Differential Gene Expression Biplot, Volcano plot, Sequence Motif output from ChIP-Seq analysis of MXTX2 transcription factor on Zebrafish embryos and Comparative Genomics analysis of genes between humans and gorillas using UCSC LiftOver.

📄 Heatmaps/ Differential Gene Expression Replicate 1.pdf and Heatmaps/ Differential Gene Expression Replicate 2.pdf

Note: Ignore the title of the plots themselves since these were unique identifier strings assigned to students of the course.

Heatmap created using High-Dimensional Data Reduction and Visualization techniques to show the gene expression levels of a Zebrafish embryo for each gene it has at different time points.

📄 Principal Component Analysis/ PC1 VS PC2.pdf and Principal Component Analysis/ PC2 VS PC3.pdf

Note: Ignore the title of the plots themselves since these were unique identifier strings assigned to students of the course.

Principal Component Analysis (PCA) plots created from NGS data of Zebrafish embryos. The two graphs are showing different Principal Components being mapped from the NGS data.

📄 Miscellaneous Visualizations/ RPKM_VS_TPM.pdf

Visual comparison created to show the relationship between the values of NGS read quantification normalization using methods of Reads-per-Kilobase Million (RPKM) and Transcripts Per Million (TPM)

Contact Information

Yogindra Raghav (YogiOnBioinformatics)

[email protected]