scImpute——An accurate and robust imputation method scImpute for single-cell RNA-seq data

An accurate and robust imputation method scImpute for single-cell RNA-seq data

http://jsb.ucla.edu/sites/default/files/publications/NC_scImpute.pdf

18年UCLA刚发在NC上的一篇technology的文章,软件试过有用但是在本人数据上并没有明显的优越性,有待更多考证。

不过原理需求甚解以便效尤后续之分析。

the workflow in the imputation step of scImpute method. scImpute first learns each gene’s dropout probability in each cell by fitting a mixture model. Next, scImpute imputes the (highly probable) dropout values in cell j (gene set Aj ) by borrowing information of the same gene in other similar cells, which are selected based on gene set Bj (not severely affected by dropout events).

 selecting matrix 的图示原理:

与其他软件的比较,空白对照和平行对照:scimpute、MAGIC、SAVER 

 

one more dimension reduction plot: 

 

clustering:

效果先摆上来,确实很不错。那么具体算法和统计模型是如何架构的呢:

step by step Factorization:

 

establishing the normalized count matrix</

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