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

TUCCA's RNA-Seq Workflow for Read Quantification, Differential Expression, and Pathway Enrichment Analysis

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

Scripts to run differential expression analysis using DESeq2 package

Probabilistic outlier identification for bulk RNA sequencing data

interactive Bioinformatics Exploratory Tools

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

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.

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

An end-to-end RNA-seq pipeline for gene expression analysis and differential expression using FASTQ data, Bowtie2, SAMtools, and R (DESeq2, Gviz, etc.).

Analysis of RNA-seq data using DESeq2

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