近来一些小伙伴留言要singleR中小鼠的注释数据集,呐,这不就来了嘛! 前面在单细胞工具箱|singleR-单细胞类型自动注释(含数据版)中介绍了singleR进行自动化注释的方法以及2个人的内置数据集,这次补充另外的5个注释数据集。 singleR自带的7个参考数据集,其中5个是人类数据,2个是小鼠的数据: BlueprintEncodeData Blueprint (Martens and Stunnenberg 2013) and Encode (The ENCODE Project Consortium 2012) (人) DatabaseImmuneCellExpressionData The Database for Immune Cell Expression(/eQTLs/Epigenomics)(Schmiedel et al. 2018)(人) HumanPrimaryCellAtlasData the Human Primary Cell Atlas (Mabbott et al. 2013)(人) MonacoImmuneData, Monaco Immune Cell Data - GSE107011 (Monaco et al. 2019)(人) NovershternHematopoieticData Novershtern Hematopoietic Cell Data - GSE24759(人) ImmGenData the murine ImmGen (Heng et al. 2008) (鼠) MouseRNAseqData a collection of mouse data sets downloaded from GEO (Benayoun et al. 2019).鼠) 以下两种获取方式,按需自取 一 ,代码获取方式
和网速和访问方式有关
remotes::install_github("LTLA/celldex") library(celldex) ref <- HumanPrimaryCellAtlasData() save(ref,file = 'HumanPrimaryCellAtlasData.Rdata') ref <- BlueprintEncodeData() save(ref,file = 'BlueprintEncodeData.Rdata') ref <- MouseRNAseqData() save(ref,file = 'MouseRNAseqData.Rdata') ref <- ImmGenData() save(ref,file = 'ImmGenData.Rdata') ref <- DatabaseImmuneCellExpressionData() save(ref,file = 'DatabaseImmuneCellExpressionData.Rdata') ref <- NovershternHematopoieticData() save(ref,file = 'NovershternHematopoieticData.Rdata') ref <- MonacoImmuneData() save(ref,file = 'MonacoImmuneData.Rdata')
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