This repo contains the analytical code to analyze two scRNA-seq data to better understand the cochlear duct extension during development

scRNA-seq datasets to support Jung et al, Sci Adv, 7(6): eabe5735, 2021. DOI: 10.1126/sciadv.abe5735

I've written a few functions that help me look through scRNA-seq data while working with Seurat.

Collection of customised plotting functions.

scRNA-seq for COVID-19 samples, with healthy controls.

An analysis of innate lymphoid cell (ILC) populations in healthy and disregulated (IBD) gut-associated samples.

Single cell app-Islets

Applying MatriCom to analyze scRNA-Seq datasets and infer ECM communication networks

Effect of temperature stress on Plasmodium Falciparum. Code for data analysis. Rshiny app for data exploration.

Differential expression analysis of CAMA-1 cells in the context of ribociclib resistance and facilitation.

DEGage is a novel model-based method for gene differential expression analysis between two groups of scRNA-seq count data. It employs a novel family of discrete distributions for describing the difference of two NB distributions (named DOTNB).

3' UTR cleavage site identification from the Mouse Cell Atlas

Code used to analyze and produce figures during tenure in the Translational Tumor Engineering Lab

Scripts and data for used in the TE Aging Manuscript

This repository contains an analysis pipeline for processing and visualizing single-cell RNA sequencing (scRNA-seq) data using the Seurat package in R. The dataset used is the Peripheral Blood Mononuclear Cells (PBMC) 3K dataset from 10X Genomics.

Investigating aging in snRNA-seq skeletal muscle data with Factor Analysis

scRNA cluster via Seurat package

Repository to store and share all related code for the Uterine macrophages and NK cells Project from the Scott Gordon Laboratory at the Children's Hospital of Philadelphia

Workflows for sc/snRNAseq from count data.