BuDDI analysis of sciplex3 data

In this zipped folder are two folders: <b>data</b> and <b>results</b><br>The sciplex data used in all of the sciplex3 analyses were downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4150378, presented in this paper: DOI: 10.1126/science.aax6234<br><b>data</b><b>data</b> contains one subfolders: <b>single_cell_data</b><b>single_cell_data</b> has the processed single-cell data and the generated pseudobulks used by BuDDI. Within this folder,<br><b>augmented_sciplex_data</b> contains the pseudobulks<b>cibersort_sciplex</b> contains the CIBERSORTx results<b>sciplex</b><b> </b>contains the processed sciplex data<b>results</b>This folder contains several results folders. Each one is specific to an experiment and a model. The naming convention is "model_CellLine". Each model learns all the drug embeddings together.<br><b>buddiM2</b>: the BuDDI model<br><b>bp</b>: BayesPrism<br><b>CVAE</b>: conditional Variational Autoencoder<br><b>PCA</b>: principal components analysis

本压缩归档文件夹包含两个子目录：<b>data</b> 与 <b>results</b>。<br>本研究所有sciplex3分析所用的sciplex数据集（sciplex）均从https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM4150378下载，其对应文献的DOI为：10.1126/science.aax6234。<br><b>data</b> 目录包含一个子目录：<b>single_cell_data</b>。<br><b>single_cell_data</b> 目录存储经预处理的单细胞数据，以及BuDDI使用的生成伪bulk数据（pseudobulks）。在此目录下：<br><b>augmented_sciplex_data</b> 目录存储伪bulk数据；<br><b>cibersort_sciplex</b> 目录存储CIBERSORTx分析结果；<br><b>sciplex</b> 目录存储经预处理的sciplex数据集。<br><b>results</b> 目录包含多个子结果目录，每个目录对应一项实验与一种模型，命名规则为"model_CellLine"，所有模型均联合学习所有药物的嵌入表示（embedding）。<br>各模型缩写对应如下：<br><b>buddiM2</b>：BuDDI模型；<br><b>bp</b>：BayesPrism模型；<br><b>CVAE</b>：条件变分自编码器（conditional Variational Autoencoder）；<br><b>PCA</b>：主成分分析（principal components analysis）