Questions tagged [scran]

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Suggestion for a single-cell analysis: how to orchestrate a single cell analysis in order to infer the cell types?

I'm very new to scRNA-seq data so I'm sorry if I eventually posed a trifling question. I orchestrated a sc-cell experiment passing through several steps. First of all I eliminated all the genes that ...
2
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3answers
360 views

How to reduce the occupied RAM when you are dealing with a very sparse matrix in a single-cell Experiment in R?

I'm dealing with a very large and sparse dataset and the first issues I met occurred when I tried to use quickCluster that reported me this error: ...
2
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1answer
210 views

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

I am using rpy2 to run normalization using scran package. After calling computeSumFactors I ...
6
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3answers
486 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
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1answer
58 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 ...
3
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1answer
298 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
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0answers
322 views

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

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