User: dppb05

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dppb0590
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Posts by dppb05

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Why different tSNE plot with Seurat and Monocle if they'r using the same R packa
... Despite both Seurat and monocle using `Rtsne` there are a few reasons the plots you got are different: * Assuming you have used their respective standard pipelines on your data: they have different pipelines which will alter the data considerably, especially in the QC part. * They are using differ ...
written 23 months ago by dppb0590
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Answer: A: Classify cells using seurat
... > Is there a similar function is Seurat. Something that allows to classify cells by cell type and adds it to the meta-data in the seurat object? There is `ClassifyCells` function. But keep in mind that this function works differently from `monocle::classifyCells`. Monocle's docs, as you have pro ...
written 23 months ago by dppb0590
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Comment: C: Seurat identify clusters associated with two time points in tSNE plot
... Do you have "day" information as a column in `object@meta.data` or do you wish to extract it first from your Seurat object and only then generate the t-SNE plot? ...
written 23 months ago by dppb0590
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Answer: A: Single cell RNA sequencing Seurat and Monocle
... You can use `monocle::importCDS` function by passing your Seurat object as parameter. ...
written 23 months ago by dppb0590
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Comment: C: plotting two genes in Seurat ScRNAseq
... @Za There are a few different ways you can do that. I suggest you create a new post with your question detailing a bit how your list of cells is stored. ...
written 23 months ago by dppb0590
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Answer: A: plotting two genes in Seurat ScRNAseq
... >Can I plot two genes simultaneously in different colors on the clusters? If it is just two genes, the `overlay` option in Seurat's `FeaturePlot` can help you with that. FeaturePlot(object = pbmc, features.plot = c("LYZ", "CD8A"), cols.use = c("grey", "blue", "red", "pink"), ...
written 2.0 years ago by dppb0590
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Answer: A: How are the p-adjusted values calculated with the compareCluster function in R?
... I will consider you are using `fun = "enrichGO"` in `compareCluster` (which is the default) and that you are not passing `pAdjustMethod` as an extra argument to `compareCluster`. From what I could understand from their source code, the short answer is that it is simply using `p.adjust` (from packag ...
written 2.0 years ago by dppb0590
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Comment: C: plotting two genes in Seurat ScRNAseq
... >Can I plot two genes simultaneously in different colors on the clusters? Let me see if I understood correctly: you wish to plot the expression of several genes, each with a different colour, in a single tSNE plot? ...
written 2.0 years ago by dppb0590
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Answer: A: question about 10x genomics output: filtered_gene_bc_matrices versus raw_gene_bc
... According to the [10X documentation](https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices): * **raw_gene_bc_matrices**: Contains every barcode from fixed list of known-good barcode sequences. This includes background and non-cellular barcodes. * ** ...
written 2.1 years ago by dppb0590
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Answer: A: Cell type assignment in single-cell RNAseq
... [Monocle][1] can do it to some extent, although it is not 100% automatic. The performance will depend on how well you define your filters (which will most likely depend on good markers for your data). Therefore you will still need to do some work (e.g. define good markers for your cell types). [ ...
written 2.1 years ago by dppb0590

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Scholar 2.1 years ago, created an answer that has been accepted. For A: question about 10x genomics output: filtered_gene_bc_matrices versus raw_gene_bc

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