Brings bulk and pseudobulk transcriptomics to the tidyverse

Transcript quantification import for modular pipelines

Statistical Analysis of RNA-Seq Tools

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

This RNAseq data analysis tutorial is created for educational purpose

DESeq2 or edgeR

a web-based R shiny application that wraps DESeq2 R package

My R scripts, primarily R plotting scripts + some genomics software including 16S rRNA metataxnomics and RNAseq

Generate HTML report for a set of genomic regions or DESeq2/edgeR results

Probabilistic outlier identification for bulk RNA sequencing data

Scripts to run differential expression analysis using DESeq2 package

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

interactive Bioinformatics Exploratory Tools

Analysis of RNA-seq data using DESeq2

R scripts used for the analysis of microbiomes associated with stony coral tissue loss disease (SCTLD) in the Florida Reef Tract

A shiny application to perform differential gene expression analysis of count data using DESeq2. The app also allows unsupervised exploration of data using PCA and hierarchical clustering.

Code for processing and analysis of TAGseq data in "The Effects of IKKβ Inhibition on Early NF-κB Activation and Transcription of Downstream Genes". Modified repository from https://github.com/z0on/tag-based_RNAseq.

R Markdown script to perform bioinformatic analysis of RNA-seq raw count matrices, including DE-testing via DESeq2 and gene set enrichment analysis (GSEA).

This repository houses the pipeline I coded to perform differential analysis of transcriptomes from two oyster species, C. gigas and C. virginica and isolate genes in the apoptosis pathway.