scRNAseq (bioconductor) data to seurat object · Biostar

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scRNAseq (bioconductor) data to seurat object

I am converting the scRNAseq data from bioconductor to Seurat object. I am not sure if my codes are correct. Thanks

My input is:

scRNAseq::PaulHSCData()

paul <- PaulHSCData()

paul_sce <- CreateSeuratObject(counts = counts(paul), meta.data = as.data.frame(colData(paul)))

Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')

paul

class: SingleCellExperiment dim: 25188 10368 metadata(0): assays(1): counts rownames(25188): 0610007L01Rik 0610007P14Rik ... mt-Nd4 rp9 rowData names(0): colnames(10368): W29953 W29954 ... W76335 W76336 colData names(13): Well_ID Seq_batch_ID ... CD34_measurement FcgR3_measurement reducedDimNames(0): altExpNames(0):

paul_sce

An object of class Seurat 25188 features across 10368 samples within 1 assay Active assay: RNA (25188 features, 0 variable features)

bioconductor seurat scrnaseq

• 1,113 views • link

updated 3.2 years ago by ATpoint

• written 3.2 years ago by Alex •

Please browse the Seurat vignettes. They have functions for automated conversion and the standard workflows cover normalization etc.

• 0 views • link

written 3.2 years ago by ATpoint

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