Comments (2)
Please, issues go in this repository: https://github.com/LTLA/SingleR
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I am trying to infer correctly cell type using SingleR. I have successfully annotated my Seurat clusters with the HPCA built-in reference (using this link) but the results seemed a bit inaccurate. Now I would like to use custom references. However I cannot find the proper tutorial. In this link, there is a chapter about custom references but I cannot find how the latter is built. I have browsed the SingleR issues (closed and open) related to this topic but only found broken url. The closest topic was this one, but it was not clear. Also I have looked into the SingleR book without finding how to create a reference. Should I start by creating a SingleR object (as described here) but then how can I use it to infer cell types? May you point at the right direction/page?
Hi I'm having the same issue. @andynkili did you come up with any solution? could you please give me some advice?
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Related Issues (20)
- can't find any of the functions related to reference data sets HOT 1
- Adding annotations HOT 2
- how to create a new reference data set HOT 4
- plotDeltaDistribution not found HOT 1
- Seurat object as input and normalization HOT 1
- Cell labeling using SingleR in seurat HOT 1
- Retrieving a list of marker genes which were used assign cell type labels to clusters HOT 1
- How to annotation cluster by singleR 1.2.4 HOT 2
- can i annotate cells in specific cell types?
- 'assay(<SingleCellExperiment>, i="character", ...)' invalid subscript 'i' 'dimnames' applied to non-array
- the Seurat3.2.2 load and SingleR 1.0.1 conflict error HOT 1
- Can't download MouseRNAseqData
- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y' HOT 4
- Error in rowAnyNAs(DelayedArray(x)) HOT 1
- SingleR() error HOT 2
- SingleR Performance Issue
- issue with input?
- discriminant features
- Questions about confidence score
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