matlab files for Tabula Microcebus

Instructions to read h5ad file in Matlab: A mat file of the complete lemur cell atlas dataset converted from the h5ad file is provided in the Figshare files. We also provide a Matlab script to import the h5ad file to mat file: please download the h5ad file of interest, Matlab script “LCA_h5ad2Mat.m” and Matlab function “read_csmatrix.m” to the same folder, and run “LCA_h5ad2Mat.m”. The mat file contains a single variable named “rawData”, a Matlab structure variable with the following fields:cells: a table of the sequenced cells with metadata for individual sequenced cells (features of the table includes above “/obs” and “/obsm” list for the h5ad file, e.g., cell_name, tissue, free_annotation_v1, and X_umap, but not the MHC counts which is included in tabMHC, see below).genes: gene tablename: NCBI gene symbol.highly_variable: whether the gene is highly variable (calculated for the entire dataset).mat_raw: a sparse matrix of the cell by gene transcript count (raw count).mat_X: a sparse matrix of the cell by gene transcript level after library size normalization and natural log transformation (i.e., smartseq2, ln(reads/N *1e4 +1); 10x, ln(UMI/N *1e4 +1), where N denotes the total number of reads or UMI of the cell).tabMHC: a table of the calculated raw counts for the major histocompatibility complex (MHC) genes (see the Tabula Microcebus manuscript for detail). Note the count is only available for cells sequenced by 10x method and count is NAN for cells sequenced by smartseq2 method. Both raw counts and normalized counts (labeled with prefix letter ‘n’) are provided.MHC_C_I, MHC_NC_I, MHC_all_II: sum of counts from classical Class I genes.nMHC_C_I, nMHC_NC_I, nMHC_all_II: sum of normalized counts from classical Class I genes.counts and normalized counts from individual classical Class I genes (Mimu_168, Mimu_W03, Mimu_W04, Mimu_249, nMimu_168, nMimu_W03, nMimu_W04, nMimu_249), non-classical Class I genes (Mimu_180ps, Mimu_191, Mimu_202, Mimu_208, Mimu_218, Mimu_229ps, Mimu_239ps, nMimu_180ps, nMimu_191, nMimu_202, nMimu_208, nMimu_218, nMimu_229ps, nMimu_239ps), and Class II genes (Mimu_DMA, Mimu_DMB, Mimu_DPA, Mimu_DPB, Mimu_DQA, Mimu_DQB, Mimu_DRA, Mimu_DRB, nMimu_DMA, nMimu_DMB, nMimu_DPA, nMimu_DPB, nMimu_DQA, nMimu_DQB, nMimu_DRA, nMimu_DRB). version: version of the data (name of the h5ad file converted from).Matlab读取h5ad文件操作指南：Figshare平台的文件库中提供了一份由该h5ad文件转换得到的完整狐猴细胞图谱数据集Mat文件。我们同时提供了将h5ad文件导入为Mat文件的Matlab脚本：请将目标h5ad文件、Matlab脚本"LCA_h5ad2Mat.m"以及Matlab函数"read_csmatrix.m"下载至同一文件夹，随后运行"LCA_h5ad2Mat.m"。该Mat文件包含一个名为"rawData"的单一变量，其为Matlab结构体变量，具备如下字段： 1. cells：包含单个测序细胞元数据的测序细胞表（该表的特征涵盖h5ad文件中"/obs"与"/obsm"列表的全部内容，例如cell_name、tissue、free_annotation_v1以及X_umap，但不包含MHC计数，相关计数收录于tabMHC，详见下文）。 2. genes：基因表，表中字段名称为NCBI基因符号。 3. highly_variable：标识基因是否为高度可变基因（基于全数据集计算得到）。 4. mat_raw：细胞×基因转录本原始计数的稀疏矩阵。 5. mat_X：经过文库大小标准化与自然对数转换后的细胞×基因转录本水平矩阵（即Smart-seq2方法：ln(reads/N ×10^4 +1)；10x方法：ln(UMI/N ×10^4 +1)，其中N代表该细胞的总读数或总UMI数）。 6. tabMHC：主要组织相容性复合体（MHC）基因原始计数计算表（详细信息参见《Tabula Microcebus》论文）。请注意，该计数仅适用于采用10x方法测序的细胞，Smart-seq2方法测序的细胞对应的计数为NAN。同时提供原始计数与以前缀字母"n"标识的标准化计数。 7. MHC_C_I、MHC_NC_I、MHC_all_II：分别为经典I类基因、非经典I类基因以及全部II类基因的计数总和。 8. nMHC_C_I、nMHC_NC_I、nMHC_all_II：分别为经典I类基因、非经典I类基因以及全部II类基因的标准化计数总和。 9. 同时提供单个经典I类基因（Mimu_168、Mimu_W03、Mimu_W04、Mimu_249，以及对应的标准化计数nMimu_168、nMimu_W03、nMimu_W04、nMimu_249）、单个非经典I类基因（Mimu_180ps、Mimu_191、Mimu_202、Mimu_208、Mimu_218、Mimu_229ps、Mimu_239ps，以及对应的标准化计数nMimu_180ps、nMimu_191、nMimu_202、nMimu_208、nMimu_218、nMimu_229ps、nMimu_239ps）与单个II类基因（Mimu_DMA、Mimu_DMB、Mimu_DPA、Mimu_DPB、Mimu_DQA、Mimu_DQB、Mimu_DRA、Mimu_DRB，以及对应的标准化计数nMimu_DMA、nMimu_DMB、nMimu_DPA、nMimu_DPB、nMimu_DQA、nMimu_DQB、nMimu_DRA、nMimu_DRB）的计数与标准化计数。 10. version：数据版本（即转换前的h5ad文件名称）。