The development of single-cell and spatial transcriptomics methods was instrumental in the conception of the Human Cell Atlas initiative, which aims to generate an integrated map of all cells across the human body. These technology advances are bringing increasing depth and resolution to maps of huma...
Integration of 17 single-cell sequencing datasets into one harmonized reference.a, UMAP visualization of HypoMap, colored by major cell types.b, UMAP of neuronal clusters in HypoMap (other cell types in gray)c, UMAP expression of key neuronal type markers and regional markers in each cell. Co...
http://biocc.hrbmu.edu.cn/CancerSEA/home.jsp Mouse Cell Atlas: http://bis.zju.edu.cn/MCA/index.html SCPortalen: http://single-cell.clst.riken.jp/ Single Cell Expression Atlas: https://www.ebi.ac.uk/gxa/sc/home SignatureDB: https://lymphochip.nih.gov/signaturedb/ KIT(肾脏单细胞数...
and obtained an atlas where marker gene expression revealed clear correspondence of the 11 putative cell types across stages (Fig.S2a, b). We focused on these shared cell types with the ultimate objective of making robust, stage-independent inferences regarding differentiation trajectories (see result...
A molecular cell atlas of the human lung from single cell RNA sequencing bioRxiv (2019), 10.1101/742320 Google Scholar Vankadari and Wilce, 2020 N. Vankadari, J.A. Wilce Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of spike glycoprotein and its interaction wit...
‘zebrafish single-cell atlas of perturbed embryos’: single-cell transcriptomic data from 1,812 individually resolved developing zebrafish embryos, encompassing 19 timepoints, 23 genetic perturbations and a total of 3.2 million cells. The high degree of replication in our study (eight or more ...
Some open-source scRNA-seq repositories or reference databases are Human Cell Atlas [98], Broad Institute's Single Cell Portal [99], EMBL-EBI's Single Cell Expression Atlas [100], PanglaoDB [101], and OmicX Jingle Bells. 10× Genomics offers datasets at various preprocessed levels for ...
?DatabaseImmuneCellExpressionData ?NovershternHematopoieticData ?MonacoImmuneData ?ImmGenData ?MouseRNAseqData ?HumanPrimaryCellAtlasData 其他的细胞类型注释流程几乎完全一样,如果后续需要个性化分析,只需要提取出自己识别好的类,然后在这些类中继续走标准流程 1-7,之后还是使用点图进行验证,单纯的只是多了个 group...
git clone https://github.com/sii-cell-atlas/paraCell.git cd paraCell source <path to Miniconda3>/etc/profile.d/conda.sh conda config --set channel_priority flexible mamba env create -n <env name, such as: paraCell> -f paraCell_conda_R.yml (local R under conda, no root privilege ...
Efficient and precise single-cell reference atlas mapping with Symphony: Kang et al. (2021) bioRxiv 2020.11.18.389189.Code Fast, sensitive and accurate integration of single-cell data with Harmony: Korsunsky et al. Nature Methods 16 (2019): 1-8.Code ...