Code to reproduce the results in the manuscript "Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis"
This repository contains the code to reproduce the results in the manuscript "Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis". The preprint can be found here.
analysis: code to generate figures in the paper
anno: code to generate and compile cell type annotation results
anno/code: code to generate cell type annotation results
anno/cl: code to populate CL terms
anno/subtype: code to identify major cell types or cell subtypes
anno/compiled: code to compile cell type annotation results
anno/process: code to process gene expression data and run sctype and SingleR
numcell: number of cells in each cell type
runtime: running time calculation
simu: code for simulation studies
supp: code to generate supplementary materials
software: in-house pipeline for sctype
Authors: Wenpin Hou (wh2526@cumc.columbia.edu) and Zhicheng Ji (zhicheng.ji@duke.edu).
Report bugs and provide suggestions by sending email to the maintainer Dr. Wenpin Hou (wh2526@cumc.columbia.edu) or open a new issue on this Github page.