Tonsil Atlas: CellRanger outputs

This repository contains all the expression and accessibility matrices for each of the five data modalities (scRNA-seq, scATAC-seq, Multiome, CITE-seq+scVDJ-seq, and spatial transcriptomics) associated with the article "An Atlas of Cells in The Human Tonsil," published in Immunity in 2024. In particular, each modality was produced with different platforms from 10X Genomics and processed with different versions of CellRanger. This repository contains the most important outputs from each CellRanger run of each library. In addition, it also includes de expression and accessiblity matrices for the two mantle cell lymphoma (MCL) patients analyzed in the paper. Version 4.0 of this repository adds all high-quality TIFF images of the Visium slides, as requested by a user.本仓库收录了与2024年发表于《免疫》（Immunity）期刊的论文《人类扁桃体细胞图谱》（An Atlas of Cells in The Human Tonsil）相关的五种数据模态的全部表达矩阵与可及性矩阵，涵盖的五种数据模态分别为：单细胞RNA测序（scRNA-seq）、单细胞转座酶可及性测序（scATAC-seq）、多组学测序（Multiome）、CITE测序联合单细胞VDJ测序（CITE-seq+scVDJ-seq）以及空间转录组学（spatial transcriptomics）。具体而言，每种数据模态均采用10X Genomics的不同平台完成测序，并通过不同版本的CellRanger进行分析处理。本仓库包含了每个文库的每一次CellRanger分析所得到的核心输出结果。此外，还收录了本论文中分析的两例套细胞淋巴瘤（MCL）患者的表达矩阵与可及性矩阵。本仓库的4.0版本应用户需求，新增了所有Visium切片的高质量TIFF图像。