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Question: is SCEset fully abandoned in scran?
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gravatar for wt215
25 days ago by
wt2150
wt2150 wrote:

The function "newSCEset()" is convenient, but I just realized that this function is deprecated. Does this mean that "SCE" is fully abandoned and now we turn to "SingleCellExperiment" for storing our scRNAseq data?

 

Thank you very much!

 

ADD COMMENTlink modified 25 days ago by davis90 • written 25 days ago by wt2150
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gravatar for davis
25 days ago by
davis90
United Kingdom
davis90 wrote:
Yes, that is correct. Both scater and scran are completely switching to SingleCellExperiment for the next Bioconductor release. The functions “toSingleCellExperiment()” and “updateSCESet()” in scater will convert an existing SCESet object to a SingleCellExperiment object for you. — Davis McCarthy NHMRC Early Career Fellow Stegle Group EMBL-EBI, Cambridge, UK www.ebi.ac.uk > On Monday, Oct 23, 2017 at 9:56 am, wt215 [bioc] <noreply@bioconductor.org mailto:noreply@bioconductor.org)=""> wrote: > Activity on a post you are following on support.bioconductor.org (https://support.bioconductor.org) > > User wt215 (wt215) wrote Question: is SCEset fully abandoned in scran? (is SCEset fully abandoned in scran? ) : > > > The function "newSCEset()" is convenient, but I just realized that this function is deprecated. Does this mean that "SCE" is fully abandoned and now we turn to "SingleCellExperiment" for storing our scRNAseq data? > > > > > > Thank you very much! > > > > > > Post tags: scran, scater, splatter, normalization > > > You may reply via email or visit is SCEset fully abandoned in scran? > > >
ADD COMMENTlink written 25 days ago by davis90

Hi Davis,

Thanks , I see. How about your paper "A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor", will you also update the code in that paper in the future? 

Many thanks!

Best wishes,

Wenhao

ADD REPLYlink written 25 days ago by wt2150

An updated version is available on the Bioconductor workflow page:

Low-level analyses of single-cell RNA-sequencing data

I will update the version on F1000Research, but this will require some time as I want to test out interactive plots with plotly.

ADD REPLYlink modified 25 days ago • written 25 days ago by Aaron Lun17k
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