Questions tagged [scran]

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1answer
72 views

AttributeError: module 'scater' has no attribute 'normalize'

I am using rpy2 to run normalization using scran package. After calling computeSumFactors I ...
6
votes
3answers
363 views

Improve scRNA-seq dataset for further analysis

I got a dataset from C.Elegans scRNA-seq paper: GSM2599701_Gene.count.matrix.celegans.cell.Rdata in ...
1
vote
1answer
40 views

Error in .checkedCall : subset indices out of range [closed]

After normalization the way it is described here: https://bioconductor.org/packages/3.7/bioc/vignettes/scran/inst/doc/scran.html Using quickCluster() function ...
2
votes
0answers
228 views

Normalization using parallel R script

I need to implement a parallel version of an R script because on one core it takes forever to execute. The function that takes the most of time is ...
1
vote
0answers
183 views

Error in .computeSumFactors: cells should have non-zero library sizes

While trying to run the following code in R: ...