Supplementary material for regionReport paper

A simple set of wrappers and tools for RNA-seq analysis. These tools were designed for the DSCI512 RNA-seq analysis class

Pipeline to process RNAseq and ChIPseq data. Outputs include gene counts, transcripts per million, alternate splicing events, SNP calls, and bigwigs. Supports both Docker and Singularity for all dependencies.

Deconvoluting mouse Immune cell fractions from Bulk RNAseq data with ImmuCell-AI_mouse

Original version of the RNA-seq pipeline implemented in SPEAQeasy at https://github.com/LieberInstitute/SPEAQeasy.

Automated Isoform Discovery Detector (AIDD)

A web resource for studying the regulation of cassette exons by human splicing factors

RNA-seq Differential Gene Expression (DGE) analysis comparing multiple dataset samples involves the comparison of gene expression levels across multiple samples with the possibliity to account for defined conditions, treatments, or groups.

Gene co-expression network analysis

Repository for the analysis of spatial gene expression in molecular subtypes of Breast Cancer

A python package for working with inputs to and outputs from the toil-rnaseq pipeline

analysis of RNA-seq data

Clustering is a common exercise to determine how closely samples are related to each other. This shows how samples can be clustered using a PCoA and PCA and visualizing using ggplot. Particularly, how to cluster RNA-seq samples.

This repo is a template for running differential gene expression analysis of RNA-seq count data followed by gene set enrichment analysis. This workflow is run in R using Rmarkdown. It is based around the popular R packages, DESeq2, fGSEA, and others.

Analysis of proteomics datasets obtained from ChIP-SICAP experiments in HEK cells

This is a script I used to make an R Shiny application that allows for browsing the time-course gene expression signal, and associated statistics, for an experiment where MCF-7 cells were exposed to oxidative stress-inducing compounds. This dataset was published in *Free Radical Biology and Medicine*, article found here https://doi.org/10.1016/j…