Reproductivity

[TimedDinner]

Hi I am trying to reproduce your results in python but I cant access your data set, I am assuming its the sce.rda file however I cant view it. Please advise

Thanks!

[yulijia]

Hi, the sce.rds file is a SingleCellExperiment object. I can load the data in R.

>library(scCCESS)
>data(sce, package = 'scCCESS')
>sce
class: SingleCellExperiment 
dim: 23433 1000 
metadata(0):
assays(1): counts
rownames(23433): 0610005C13Rik 0610007C21Rik ... l7Rn6 zsGreen_transgene
rowData names(0):
colnames(1000): B12.MAA000938.3_8_M.1.1 O20.MAA000614.3_10_M.1.1 ...
  E10.D043526.3_39_F.1.1 H1.MAA000508.3_9_M.1.1
colData names(2): cellTypes sizeFactor
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):

I am not sure the reason why you cannot view it?

[TimedDinner]

Is this the file with the raw data used for analysis? I am trying to replicate your results using the dataset from this repo. Is it possible for me to acquire the csv file of the data you used?

[yulijia]

Hi,

sce.rds is real scRNAseq demo data that you can use to run the scCCESS package