Codes for reproducing the experiments of the paper "Adversarial domain translation networks for fast and accurate integration of large-scale atlas-level single-cell datasets". Portal package.
- Integration of mouse spleen datasets (we reproduce the result of performance metrics in this notebook as an example). Benchmarking.
- Integration of mouse marrow datasets.
- Integration of mouse bladder datasets.
- Integration of mouse brain cerebellum datasets.
- Integration of mouse brain hippocampus datasets.
- Integration of mouse brain thalamus datasets.
- Integration of human PBMC datasets (sensitivity analysis).
- Integration of entire mouse cell atlases from the Tablula Muris project.
- Integration of mouse brain scRNA-seq and snRNA-seq datasets.
- Integration of human PBMC scRNA-seq and human brain snRNA-seq datasets.
- Integration of scRNA-seq and scATAC-seq datasets.
- Integration of developmental trajectories.
- Integration of spermatogenesis differentiation process across multiple species. Gene lists from Ensembl Biomart (we only use genes that are assigned with the type "ortholog_one2one" in the lists): orthologues (human vs mouse), orthologues (human vs macaque).
Jia Zhao, Gefei Wang, Jingsi Ming, Zhixiang Lin, Yang Wang, The Tabula Microcebus Consortium, Angela Ruohao Wu, Can Yang. Adversarial domain translation networks for integrating large-scale atlas-level single-cell datasets. Nature Computational Science 2, 317–330 (2022). https://doi.org/10.1038/s43588-022-00251-y.