Protocol data (Python version)

We published 3 protocols illustrating how MetaNeighbor can be used to quantify cell type replicability across single cell transcriptomic datasets.<br>The data files included here are needed to run the Python version of the protocols available on Github (https://github.com/gillislab/MetaNeighbor-Protocol) in Jupyter (.ipynb) notebook format. To run the protocols, download the protocols on Github, download the data on Figshare, place the data and protocol files in the same directory, then run the notebooks in Jupyter.<br>Briefly:- biccn_hvg.h5ad contains a single cell transcriptomic dataset published by the Brain Initiative Cell Census Network (in AnnData format). It combines data from 7 datasets obtained in the mouse primary motor cortex (https://www.biorxiv.org/content/10.1101/2020.02.29.970558v2). Note that this dataset only contains highly variable genes.- biccn_gaba.h5ad: same dataset as biccn_hvg.h5ad, but restricted to GABAergic neurons. The dataset contains all genes common to the 7 BICCN datasets (not just highly variable genes).- hemberg.h5ad contains a merged version of 4 human pancreas single cell transcriptomic datasets made available in a standardized form by the Hemberg lab.- tasic.h5ad contains a single cell transcriptomic dataset of neurons from the mouse primary visual cortex, as published in Tasic et al. 2016.- go_mouse.mtx, go_mouse_col_labels.txt, go_mouse_row_labels.txt: mouse gene ontology annotations, stored as a one-hot encoded matrix.

我们发布了3套实验方案，用以演示如何借助MetaNeighbor量化不同单细胞转录组数据集间的细胞类型可复制性。
本文提供的数据文件是运行GitHub（https://github.com/gillislab/MetaNeighbor-Protocol）上以Jupyter Notebook（.ipynb）格式发布的Python版方案所需的依赖文件。使用该方案时，请先从GitHub下载方案文件、从Figshare下载数据集文件，将二者置于同一目录下，随后在Jupyter环境中运行对应Notebook即可。
简要说明如下：
- `biccn_hvg.h5ad`：由脑计划细胞普查网络（Brain Initiative Cell Census Network, BICCN）发布的单细胞转录组数据集，以AnnData格式存储。该数据集整合了小鼠初级运动皮层的7项单细胞转录组数据（来源：https://www.biorxiv.org/content/10.1101/2020.02.29.970558v2）。请注意，此数据集仅包含高可变基因。
- `biccn_gaba.h5ad`：与`biccn_hvg.h5ad`为同一数据集，但仅包含γ-氨基丁酸能神经元（GABAergic neurons）数据。该数据集涵盖了7项BICCN数据集共有的全部基因（而非仅高可变基因）。
- `hemberg.h5ad`：整合了4项人类胰腺单细胞转录组数据集的合并数据集，由亨伯格实验室（Hemberg lab）以标准化格式发布。
- `tasic.h5ad`：来自小鼠初级视觉皮层神经元的单细胞转录组数据集，对应Tasic等人2016年发表的研究成果。
- `go_mouse.mtx`、`go_mouse_col_labels.txt`与`go_mouse_row_labels.txt`：小鼠基因本体（Gene Ontology, GO）注释文件，以独热编码矩阵形式存储。