Questions tagged [scran]
The scran tag has no usage guidance.
6
questions
6
votes
3
answers
594
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 ...
3
votes
1
answer
366
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 ...
2
votes
4
answers
733
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
votes
1
answer
442
views
AttributeError: module 'scater' has no attribute 'normalize'
I am using rpy2 to run normalization using scran package. After calling computeSumFactors I ...
1
vote
1
answer
61
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 ...
1
vote
0
answers
437
views
Error in .computeSumFactors: cells should have non-zero library sizes
While trying to run the following code in R:
...