Zhu et al. "Defective human somitogenesis in the absence of HOX genes" scRNA-Seq analysis

Zhu et al. "Defective human somitogenesis in the absence of HOX genes" scRNA-Seq analysis Code used for the 10x scRNA-Seq analysis in the manuscript *"Defective human somitogenesis in the absence of HOX genes"* by Zhu et al. All fastq and count matrices have been deposited in GEO under the accession number GSE288370 This repository contains the following jupyter notebooks organized by theme: Analysis of the WT sample: 20240924_HOXWT-individualanalysis-Upload Analysis of the HOXKO sample: 20241108_HOXKO-individualanalysis-Upload Merging of all the samples followed by regression and scaling : 20241109_HOX_singlecell_project-regscalling-Upload Merging of all the samples followed by regression and scaling and Harmony Integration : 20241013_HOX_singlecell_project-Upload 20241017_HOX_singlecell_project-Downstream_Upload 20241017_HOX_singlecell_project-Subsampling-Upload Additional plots requested during the revision process: 20251220_HOX_singlecell_revision-Upload 20251220_HOX_singlecell_revision-part2_Upload Miscellaneous code:- 20250108_HOXproject_UMAP_coloring-Upload Software / key packagesAnalyses were run in Python 3.9.18 (packaged by conda-forge) using the following key packages: - scanpy 1.10.0- anndata 0.10.7- numpy 1.23.0- pandas 2.2.2- scipy 1.13.0- matplotlib 3.8.0- jupyterlab 4.1.1- notebook 7.1.0 The list of dependencies can be found in each notebook uploaded. We also provide processed AnnData .h5ad files to reproduce the figures.