SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data
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Processed data for the manuscript "" available on bioRxiv at "" Data is available for the following samples CD34+ Multiome data : 2 replicates T-cell depleted bone marrow Multiome data: 2 replicates The following counts and fragments files are available for each replicate <sample>_filtered_feature_bc_matrix.h5: Feature counts from CellRanger ARC <sample>_atac_fragments.tsv.gz: ATAC fragments file from Cellranger ARC <sample>_atac_fragments.tsv.gz.tbi: Index files for ATAC fragments file from Cellranger ARC The following scanpy anndata objects are also available cd34_multiome_rna.h5ad: Anndata object with normalized data, cell type annotations and clusters for the RNA modality of CD34+ hematopoietic stem and progenitor cells cd34_multiome_atac.h5ad: Anndata object with peak counts, cell type annotations and clusters for the ATAC modality of of CD34+ hematopoietic stem and progenitor cells. cd34_multiome_rna.h5ad: Anndata object with normalized data, cell type annotations and clusters for the RNA modality of T-cell depleted bone marrow dataset. bm_multiome_atac.h5ad: Anndata object with peak counts, cell type annotations and clusters for the ATAC modality of T-cell depleted bone marrow dataset.
本数据集对应bioRxiv平台上一篇未提供链接的手稿的处理后数据，可获取的样本数据分为两类：CD34+ 多组学（Multiome）数据（含2次生物学重复），以及T细胞耗竭骨髓多组学数据（含2次生物学重复）。针对每个重复样本，可获取以下计数与片段文件： 1. <sample>_filtered_feature_bc_matrix.h5：来自CellRanger ARC的特征计数文件 2. <sample>_atac_fragments.tsv.gz：来自CellRanger ARC的ATAC测序片段文件 3. <sample>_atac_fragments.tsv.gz.tbi：来自CellRanger ARC的ATAC测序片段文件索引文件 此外还提供以下Scanpy配套的AnnData对象： 1. cd34_multiome_rna.h5ad：包含CD34+造血干祖细胞RNA模态的标准化数据、细胞类型注释及聚类信息的AnnData对象 2. cd34_multiome_atac.h5ad：包含CD34+造血干祖细胞ATAC模态的峰计数、细胞类型注释及聚类信息的AnnData对象 3. cd34_multiome_rna.h5ad：包含T细胞耗竭骨髓数据集RNA模态的标准化数据、细胞类型注释及聚类信息的AnnData对象 4. bm_multiome_atac.h5ad：包含T细胞耗竭骨髓数据集ATAC模态的峰计数、细胞类型注释及聚类信息的AnnData对象
