Training_sc

This dataset contains various scRNA-seq datasets that are used in the omnideconv benchmarking study. Each dataset is stored as a SummarizedExperiment object in RDS format (compressed file format for R).The objects contain the following data:[assay] 'counts': raw gene expression counts[assay] 'tpm': CPM-normalized gene expression counts[metadata] 'batch': batch information of samples in dataset[metadata] 'cell_type': the cell-type annotation that was used in the benchmark. Often, this included manual refinement and filtering of the original dataset. Some datasets contain annotations with different resolution levels (fine, coarse).<br>Included datasets are:Hao: blood, human [https://doi.org/10.1038/s41591-021-01329-2]HaoSub: subset of Hao, 10% of each cell-typeWu: breast cancer, human [https://doi.org/10.1038/s41588-021-00911-1]Allen: brain post-mortem, human [https://doi.org/10.1038/s41586-021-03465-8]TabulaSapiens: blood, human [https://doi.org/10.1126/science.abl4896]Lambrechts: lung cancer, human [https://doi.org/10.1038/s41591-018-0096-5]SchulteSchrepping: blood, human [https://doi.org/10.1016/j.isci.2021.103115]Arunachalam: blood, human [https://doi.org/10.1016/j.isci.2021.103115]Heimlich: blood, human [https://doi.org/10.1182/bloodadvances.2023011445]DominguezConde: blood, human [https://doi.org/10.1126/science.abl5197]Maynard: lung cancer, human [https://doi.org/10.1016/j.cell.2020.07.017]Lee: blood, human [https://doi.org/10.1126/sciimmunol.abd1554]TabulaMuris: spleen, mouse [https://doi.org/10.1038/s41586-018-0590-4]<br>