is SCEset fully abandoned in scran?
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wt215 • 0
@wt215-12405
Last seen 2.9 years ago

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!

 

scran scater splatter normalization • 1.4k views
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davis ▴ 90
@davis-8868
Last seen 4.0 years ago
United Kingdom
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? > > >
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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

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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.

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