Projects

This is a small selection of my personal and professional projects as of 2021-07-25:

1. 10X Seurat Single Cell Visualization Pipeline
This pipeline performs analysis of 10X single cell RNAseq data using the Seurat package, producing diagnostic visualizations and statistics.

2. depmap
The depmap Bioconductor package stores data from data from the Depmap project, formatting this data for use of popular R data analysis and visualizing tools such as dplyr and ggplot2. This package utilizes ExperimentHub, accessing versions of the Depmap data from the Cloud.

3. RNAseq NGS Snakemake Pipeline
This Snakemake pipeline automates a RNAseq workflow utilizing bash command line tools (fastqc, trimmomatic, histat2 and htseq-count), starting with paired-end fastq.gz files and outputing a count matrix for differential expression analysis. This pipeline utilizes Conda to maintain a software environment that ensures data reproducibility.

4. Transcriptomic DE Result Shiny Apps
This interactive web app allows users to explore the results of differential expression analysis through dynamic visualizations and customizable html tables.

5. RNAseq analysis of miRNA targeting sarcoma oncogenes in humans and mice
DESeq2 RNAseq differential expression analysis of human and mouse samples with the objective of comparing the expression profiles of sarcoma oncogenes between the two species in order to develop a targeted miRNA sarcoma therapy.