Import and summarize transcript-level estimates for gene-level analysis

Brings transcriptomics to the tidyverse

Statistical Analysis of RNA-Seq Tools

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

DESeq2 or edgeR

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

Differential gene expression analysis and pathway analysis of RNAseq data

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

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

A computational pipeline for bulk ATAC-seq (or RNA-seq)

This tutorial is created for educational purpose

Public repo for the recount Bioconductor workflow that is visible at http://bioconductor.org/help/workflows/

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.

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

A quick recap of widely used differential analyses methods in R for RNA-seq experiments

single cell and bulk RNASeq analysis scripts

Repository miscellaneous R scripts including scripts for RNAseq analysis

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

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.

🛠 under active development | RNA-Seq Workflow in Jupyter Notebook

Perform differential analysis from FastQ files with Salmon, tximport, and DESeq2

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.

Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.

Galaxy wrappers for SARTools (Statistical Analysis of RNA-Seq Tools)

Package for the recount workshop for BioC2017

Pipeline of somatic variant analysis using Waldenstrom macroglobulinemia patient’s RNA-seq data, including tools like STAR, HTseq, VarScan in parallel computing in SGE clusters, Deseq2 and GSEA in R

Análise de RNA-seq - Abundância de Transcritos Utilizando kallisto, tximport e DESeq2

Analysis of RNA-seq data using DESeq2