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 |CellScope 源代码 本源代码用于复现《CellScope：基于树状结构表征的高性能细胞图谱工作流》一文中的实验结果。 CellScope 软件 为方便学界使用，我们提供了基于Python的实现版本。如需查看教程及其他细节，请访问我们的官网：https://cellscope.readthedocs.io/en/latest/。 数据集信息 CellScope 共采用36个基准数据集，具体信息详见下表。我们已将全部36个数据集的基因表达矩阵与细胞标签存储于Data文件夹中。此外，Code文件夹内包含`Calculate_ARI.ipynb`文件，该文件涵盖了数据导入代码，以及基于调整兰德指数（Adjusted Rand Index, ARI）计算聚类精度的程序。 | 数据代码 | 数据集名称 | 组织类型 | 发表年份 | 细胞数 | 基因数 | 细胞类型数 | | --- | --- | --- | --- | --- | --- | --- | | GSE36552 | Yan | 人类胚胎 | 2013 | 90 | 20214 | 6 | | E-MTAB-3321 | Goolam | 小鼠胚胎 | 2016 | 124 | 41428 | 5 | | SRP041736 | Pollen | 人类大脑 | 2014 | 249 | 14805 | 11 | | GSE83139 | Wang | 人类胰腺 | 2016 | 457 | 19950 | 7 | | GSE67835 | Darmanis | 人类大脑 | 2015 | 466 | 22088 | 9 | | GSE59739 | Usoskin | 小鼠腰椎组织 | 2015 | 622 | 25334 | 4 | | GSE81608 | Xin | 人类胰岛 | 2016 | 1600 | 39851 | 8 | | GSE132042-Intestine | Keller(I) | 小鼠肠道 | 2019 | 1887 | 17985 | 5 | | GSE85241 | Muraro | 人类胰腺 | 2016 | 2126 | 19127 | 10 | | PHS000424V9P2-Brain | NHGRI | 人类大脑 | 2022 | 2642 | 14717 | 8 | | GSE65525 | Klein | 小鼠胚胎 | 2015 | 2717 | 24175 | 4 | | GSE60361 | Zeisel | 小鼠大脑皮层 | 2015 | 3005 | 19972 | 7 | | PHS000833 | Lake | 人类大脑 | 2018 | 3042 | 25051 | 16 | | GSE132042-Pancreas | Keller(P) | 小鼠胰腺 | 2019 | 3384 | 21069 | 9 | | GSE108097-Brain | Han(B) | 小鼠大脑 | 2018 | 4038 | 16906 | 15 | | SCR015820-MidBrain | Siletti-1 | 人类大脑 | 2023 | 4714 | 59357 | 11 | | GSE103322 | Tirosh | 人类口腔组织 | 2017 | 5902 | 23686 | 10 | | SCR015820-LNC | Siletti-2 | 人类大脑 | 2023 | 6877 | 59357 | 10 | | GSE84133-Human | Baron(H) | 人类胰腺 | 2016 | 8569 | 20125 | 14 | | SCR015820-Pons | Siletti-3 | 人类大脑 | 2023 | 23349 | 59236 | 13 | | SCR015820-THM | Siletti-4 | 人类大脑 | 2023 | 27111 | 59236 | 11 | | SCR015820-HiB | Siletti-5 | 人类大脑 | 2023 | 28724 | 59236 | 12 | | SCR015820-Pn | Siletti-6 | 人类大脑 | 2023 | 47416 | 59236 | 13 | | GSE178101 | Ulrich(H) | 人类输卵管 | 2021 | 59738 | 36960 | 12 | | E-MTAB-13382 | Li | 人类滋养层类器官 | 2024 | 67996 | 36398 | 3 | | --- | Li(H) | 人类视网膜 | 2023 | 72788 | 36398 | 13 | | GSE228590-LA | Qiu(L) | 小鼠胚胎组织 | 2024 | 76732 | 45854 | 6 | | GSE178101 | Ulrich | 人类输卵管 | 2021 | 77536 | 36960 | 12 | | GSE228590-EO | Qiu(E) | 小鼠胚胎组织 | 2024 | 93695 | 45854 | 11 | | GSE160189 | Ayhan | 海马组织 | 2021 | 129905 | 17132 | 8 | | GSM5027160 etc | Posner | 人类大脑 | 2022 | 130908 | 25232 | 16 | | GSE243413 | Li(M) | 小鼠视网膜 | 2024 | 147523 | 32034 | 13 | | E-MTAB-10187 | Yu | 人类多内胚层组织 | 2021 | 155232 | 30867 | 20 | | E-MTAB-12795 | Hoo | 人类胎盘 | 2024 | 158978 | 36398 | 7 | | SCR016152-2 | Yao | 小鼠运动皮层 | 2021 | 159738 | 30511 | 11 | | --- | Li(HA) | 人类视网膜 | 2023 | 265767 | 36398 | 18 |