scRNAseq包整理好的单细胞数据集你都处理了一遍吗？

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我们以前就提到过：很多出名的单细胞数据集，比如Pollen et al. 2014 数据集，本质上属于地址为https://hemberg-lab.github.io/scRNA.seq.datasets/human/tissues/ ，的宝藏网页。

宝藏网页

也就是说，很多单细胞转录组数据集，都是被scRNAseq包整理好了，比如Pollen et al. 2014 数据集，使用scRNAseq包的函数ReprocessedFluidigmData() 就可以下载该数据集：

library(scRNAseq)
fluidigm <- ReprocessedFluidigmData()
fluidigm

这个包 里面的全部数据集如下；

[1] "AztekinTailData()" "BachMammaryData()" "BaronPancreasData('human')" 
 [4] "BaronPancreasData('mouse')" "BuettnerESCData()" "CampbellBrainData()" 
 [7] "ChenBrainData()" "GrunHSCData()" "GrunPancreasData()" 
[10] "HermannSpermatogenesisData()" "HuCortexData()" "KolodziejczykESCData()" 
[13] "LaMannoBrainData('human-es')" "LaMannoBrainData('human-embryo')" "LaMannoBrainData('human-ips')" 
[16] "LaMannoBrainData('mouse-adult')" "LaMannoBrainData('mouse-embryo')" "LawlorPancreasData()" 
[19] "LengESCData()" "LunSpikeInData('416b')" "LunSpikeInData('tropho')" 
[22] "MacoskoRetinaData()" "ReprocessedTh2Data()" "MairPBMCData()" 
[25] "KotliarovPBMCData()" "MarquesBrainData()" "MessmerESCData()" 
[28] "MuraroPancreasData()" "NestorowaHSCData()" "PaulHSCData()" 
[31] "ReprocessedFluidigmData()" "RichardTCellData()" "RomanovBrainData()" 
[34] "SegerstolpePancreasData()" "ShekharRetinaData()" "StoeckiusHashingData(mode='mouse')"
[37] "StoeckiusHashingData(mode='human')" "StoeckiusHashingData(type='mixed')" "UsoskinBrainData()" 
[40] "TasicBrainData()" "ReprocessedAllenData()" "WuKidneyData()" 
[43] "XinPancreasData()" "ZeiselBrainData()" "ZilionisLungData()" 
[46] "ZilionisLungData('mouse')"

可以在网络情况好的时候，批量下载哦！

library(scRNAseq) 
out <- listDatasets() 
lapply( out$Call , function(x){
 pro= gsub("'",'-', gsub('[()]','', x ))
 print(pro)
 f=paste0( pro ,
 '.Rdata')
 if( ! file.exists(f)){
 sce=eval(parse(text=x))
 save(sce,file = f)
 } 
})

可以看到，数据量并不大！全部保存好，慢慢做！

数据量并不大

六月份我们安排学徒们做了20篇数据挖掘文献的图表复现，这个月我们准备安排学员们开始做这个scRNAseq包整理好的单细胞转录组数据集的分析！

敬请期待

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