Gene expression on C. elegans single cells

A single-cell atlas of the murine limb skeleton integrating the developmental and adult stages

hatpal is an R package for alternative polyadenylation (APA) identification & analysis using 3’ scRNA-seq (10x etc.).

A utility designed to assess the performance of various tools in detecting highly variable genes in scRNAseq data

Repo linked to our recent publication in Science Advances

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

Analysis of single cell RNAseq data from stimulated iPSC-derived microglia

A effort to collect all of the scRNA imputation methods and allow them to interface with scRNA-seq libraries (i. e. Seurat, SingleCellAssay, etc...)

adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data

Single-Cell Data Science

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.

Code for exploration of non-coding elements in single-cell RNA seq data

Integrated Analysis of CircRNA Regulation with ADARB2 Enrichment in Inhibitory Neurons (Computers in Biology and Medicine, 2024)

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

ThunderBio scRNA-seq pipeline

BCF's single-cell GEX analysis workflows and Shiny App source code

Small repo for running Allen Institute's Cell_Type_Mapper (MapMyCells) on Seurat scRNAseq objects.

scCTS: identifying the cell type-specific marker genes from population-level single-cell RNA-seq