Script to automate differential expression analysis using DESeq2, edgeR or limma-voom

The package RNAseqAnalysis does the complete analysis of RNA seq data starting from raw reads. It provides the user with differnt functions like generation of qc report, filtering, assembly and GO-term annotation, differential expression analysis and heatmap generation, and Alternative splicing-site prediction

Code and figures for the Differential Causal Inference (DCI) algorithm

DEMUX, ALIGN, DESEQ2 DGE CALLS

Workshops, Course Schedule and Teaching Assistant Review from my time as a chosen Undergraduate Teaching Assistant for the University of Pittsburgh course, BIOSC1540 - Computational Genomics taught by Dr. Miler Lee.

Scripts to run differential expression analysis using DESeq2 package

Complete Pipeline for RNA-seq data analysis: From FastQ to differntial gene expression to annotated Variations.

RNA-seq analysis pipeline

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

Viper is a Snakemake workflow, aimed at performing the RNA-seq workflow of the paper 'Causes and consequences of a glutamine induced normoxic HIF1 activity for the tumor metabolism', Kappler et al. (2019) in a reproducible and automated manner

Bayesian Gene Selection Criterion (BGSC) approach

These are tutorials on a subset of tools available for processing raw RNAseq data. This if for HISAT2_SAMtools_Stringtie_gffcompare_ballgown pipeline or HISAT2_SAMtools_Stringtie_PrepDEanalysis.py_DESeq2 pipeline

🍊 View the gene expression response to TNF and IL-17A with vanilla Javascript and HTML.

GSE147507 SARS-Cov-2 Dataset from Mt. Sinai

Bioinformatic scripts for working on the UiO Abel compute cluster

RNA-Seq data analysis: Quantification, Differential Gene Expression, Differential Transcripts Usage

Performed a differential gene expression analysis with RNA-seq on three immunologically diverse mouse models. Differentially expressed genes were identified and a GO term enrichment analysis was done to determine their roles.

An R package: RNA structure and Expression analysis

Example R Shiny app demonstrating Seven Bridges Platform integration via OAuth2.

Differential Gene Analysis of Telomere Microarray Data