Source data of CellScope

CellScope source code The source code for the reproduction of results in "CellScope: High-Performance Cell Atlas Workflow with Tree-Structured Representation". Software CellScope We provide a Python-based implementation for the convenience of the community. For tutorials and other details, check our website: https://cellscope.readthedocs.io/en/latest/. Data Information CellScope utilizes 36 benchmark datasets, with specific information detailed in the table below. We have provided the gene expression matrices and labels for all 36 datasets in the Data folder. Additionally, the Code folder contains `Calculate_ARI.ipynb`, which includes both data import code and a program for calculating clustering accuracy using the Adjusted Rand Index (ARI). | Data Codes | Data Name | Tissue | Year | Num of Cells | Num of Genes | Num of Cell types || ------------------- | --------- | --------------------------- | ---- | ------------ | ------------ | ----------------- || GSE36552 | Yan | Human Embryos | 2013 | 90 | 20214 | 6 || E-MTAB-3321 | Goolam | Mouse Embryos | 2016 | 124 | 41428 | 5 || SRP041736 | Pollen | Human Brain | 2014 | 249 | 14805 | 11 || GSE83139 | Wang | Human Pancreatic | 2016 | 457 | 19950 | 7 || GSE67835 | Darmanis | Human Brain | 2015 | 466 | 22088 | 9 || GSE59739 | Usoskin | Mouse Lumbar | 2015 | 622 | 25334 | 4 || GSE81608 | Xin | Human Islet | 2016 | 1600 | 39851 | 8 || GSE132042-Intestine | Keller(I) | Mouse Intestine | 2019 | 1887 | 17985 | 5 || GSE85241 | Muraro | Human Pancreas | 2016 | 2126 | 19127 | 10 || PHS000424V9P2-Brain | NHGRI | Human Brain | 2022 | 2642 | 14717 | 8 || GSE65525 | Klein | Mouse Embryos | 2015 | 2717 | 24175 | 4 || GSE60361 | Zeisel | Mouse Cerebral Cortex | 2015 | 3005 | 19972 | 7 || PHS000833 | Lake | Human Brain | 2018 | 3042 | 25051 | 16 || GSE132042-Pancreas | Keller(P) | Mouse Pancreas | 2019 | 3384 | 21069 | 9 || GSE108097-Brain | Han(B) | Mouse Brain | 2018 | 4038 | 16906 | 15 || SCR015820-MidBrain | Siletti-1 | Human Brain | 2023 | 4714 | 59357 | 11 || GSE103322 | Tirosh | Human oral cavity | 2017 | 5902 | 23686 | 10 || SCR015820-LNC | Siletti-2 | Human Brain | 2023 | 6877 | 59357 | 10 || GSE84133-Human | Baron(H) | Human Pancreas | 2016 | 8569 | 20125 | 14 || SCR015820-Pons | Siletti-3 | Human Brain | 2023 | 23349 | 59236 | 13 || SCR015820-THM | Siletti-4 | Human Brain | 2023 | 27111 | 59236 | 11 || SCR015820-HiB | Siletti-5 | Human Brain | 2023 | 28724 | 59236 | 12 || SCR015820-Pn | Siletti-6 | Human Brain | 2023 | 47416 | 59236 | 13 || GSE178101 | Ulrich(H) | Human Fallopian Tubes | 2021 | 59738 | 36960 | 12 || E-MTAB-13382 | Li | Human Trophoblast Organoids | 2024 | 67996 | 36398 | 3 || --- | Li(H) | Human Retina | 2023 | 72788 | 36398 | 13 || GSE228590-LA | Qiu(L) | Mouse Embryonic | 2024 | 76732 | 45854 | 6 || GSE178101 | Ulrich | Human Fallopian Tubes | 2021 | 77536 | 36960 | 12 || GSE228590-EO | Qiu(E) | Mouse Embryonic | 2024 | 93695 | 45854 | 11 || GSE160189 | Ayhan | Hippocampal | 2021 | 129905 | 17132 | 8 || GSM5027160 etc | Posner | Human Brain | 2022 | 130908 | 25232 | 16 || GSE243413 | Li(M) | Mouse Retina | 2024 | 147523 | 32034 | 13 || E-MTAB-10187 | Yu | Human Multi-Endodermal | 2021 | 155232 | 30867 | 20 || E-MTAB-12795 | Hoo | Human Placenta | 2024 | 158978 | 36398 | 7 || SCR016152-2 | Yao | Mouse Motor Cortex | 2021 | 159738 | 30511 | 11 || --- | Li(HA) | Human Retina | 2023 | 265767 | 36398 | 18 |