Analysis notebooks and data used in the manuscript:
"Gene-level alignment of single cell trajectories"
https://www.biorxiv.org/content/10.1101/2023.03.08.531713v3 (bioRxiv Preprint)
Available datasets:
- Simulated trajectories using Gaussian Processes
- Simulated trajectory perturbations using the mouse pancreas development dataset from CellRank (https://github.com/theislab/cellrank).
- Negative control simulated dataset generated using the published script of Laidlaw et al (2023) at https://github.com/No2Ross/TrAGEDy.
- Anndata objects of the PAM/LPS-treated murine bone marrow-dreived dendritic cell dataset of Shalek et al. (2014) compiled from the datafiles at https://github.com/shenorrLabTRDF/cellAlign.
- Preprocessed and analysed Healthy/IPF datasets:
(original raw data of Adams et al. (2020) downloaded from GEO: GSE136831). - Preprocessed and analysed Pan fetal reference datasets:
(original raw data of Suo et al. (2022) downloaded from https://developmental.cellatlas.io/fetal-immune). - Preprocessed and analysed Artificial thymic organoid datasets:
(raw sequencing data available from ArrayExpress: E-MTAB-12720). - Additional data files: Human transcription factor list (Lambert et al. 2018) , cell-cycle gene list (Regev Lab), and relevant Gene Ontology pathway gene sets.
Large data objects are available at: https://zenodo.org/records/11182400
All analysis notebooks use Genes2Genes v0.1.0 (https://github.com/Teichlab/Genes2Genes/releases/tag/v0.1.0)