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3 votes

Can 5' end 10x be used instead of 3' end

It depends on the task. If you want to recover TCR and BCR repertoires along with gene expression - 5' is a must. Also, for an overview repertoire analysis you dont even have to perform target ...
Mark Izraelson's user avatar
2 votes
Accepted

umap failed to cluster the cells

Without more code and data, this can't be debugged. But first question would be does the data pass basic QC (e.g. look at cellranger web summaries or equivalent). If yes, you could trying different ...
Chris_Rands's user avatar
  • 3,858
2 votes

How to identify a low proportion cell subpopulation in the single-cell RNA-seq data?

Run the usual steps including clustering and visualization via something like UMAP and then color the UMAP by these four markers. That assumes that the surface marker separation you see in flow holds ...
ATpoint's user avatar
  • 551
2 votes
Accepted

Cellranger results have too many cells

The Barcode Rank plot shows very high background in your sample. The cell estimation from Cell Ranger will look for a sudden drop in the number of UMIs and use this ...
PPK's user avatar
  • 858
1 vote
Accepted

Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amount of mRNA in given cell?

I am inclined to agree with you that the reads-per-cell is dependent on the cell type and cell cycle state. In the datasets I have analyzed, I observed that immune cells tend to have far fewer reads ...
GWW's user avatar
  • 752
1 vote
Accepted

h5ad file format filter

You didn't show us how the original .h5ad object was generated, how you read it in, how you wrote it, and if you did anything else in-between besides filtering. ...
Chris_Rands's user avatar
  • 3,858
1 vote

h5ad file format filter

Scanpy's h5ad is in fact hdf5 format. This format is used for rapid read/write (i/o) large amounts of data and thats its purpose. Its fairly easy to use from ...
M__'s user avatar
  • 10.2k
1 vote

How to calculate cell type percentage in every sample

The following package performs this type of analysis and can be directly used on a Seurat object: paper: propeller: testing for differences in cell type proportions in single cell data github: Speckle ...
Macintosh's user avatar
  • 158
1 vote

How to calculate cell type percentage in every sample

If your cell types and sample names are in separate metadata variables attached to the Seurat object, then you can use table to count up the pairings: ...
gringer's user avatar
  • 13k
1 vote

How to do pathway analysis after scanpy for single cell data after DE analysis?

An easy way to do an enrichment analysis in scanpy is using scanpy.queries.enrich(). This relies on gprofiler, which uses KEGG, GO and other ontologies
Chris_Rands's user avatar
  • 3,858
1 vote
Accepted

How many percents explained variance by the first 50 principal components of PCA analysis is suitable for downstream `KNN` and `umap`?

Edit To answer the question, you're looking for 80% variance .... from the comments the actual command is np.cumsum which changes things a lot. Previous response ......
M__'s user avatar
  • 10.2k
1 vote
Accepted

Best method to compare differentially expressed genes between 2 single cell clusters for GSEA

I wish to focus my contribution singly on ScanPy vs. Seurat FindMarkers. ScanPy's claim is it is essentially a speeded up version of Seurat FindMarkers with better performance (discussed below) ...
M__'s user avatar
  • 10.2k
1 vote
Accepted

How to preserve colour assignments in matplotlib when a category is empty?

My recommendation is to report the issue directly on the ScanPy Github page here: https://github.com/scverse/scanpy/issues This is a shortcoming with the testing of ...
M__'s user avatar
  • 10.2k
1 vote

FlowSOM multi-step clustering

The two step approach will be used in any cluster algorithm (except see "network theory" below), you just may not see it. Clustering methods are very common in genomics, they are popular ...
M__'s user avatar
  • 10.2k
1 vote
Accepted

How to extend the x axis in Dimplot Seurat

Looking at the source code for Seurat's DimPlot() it's based on ggplot2 graphics (https://github.com/satijalab/seurat/blob/HEAD/R/visualization.R#L794), so you can ...
jared_mamrot's user avatar
1 vote
Accepted

Definition of genotype in demuxlet

The genotypes $\{0,1,2\}$ are mappings to the genotypes AA (homref), AB (heterozygous), BB (homalt) (from supplementary resources). This is also mapped to the number of alterations (e.g., 0 -> 0 ...
gc5's user avatar
  • 1,773
1 vote

Error in dimnamesGets(x, value) when trying to read data using Seurat package

There is a mismatch of 1 line between the several files, suggesting that probably either the barcodes of features file has a header line which is not standard. Remove any header lines from these files....
scrnaseqer's user avatar
1 vote

Error in dimnamesGets(x, value) when trying to read data using Seurat package

Check the length of your files. The error clearly says that there is a difference in the length of your files. Your file length should be equal. I think the problem may be the presence of a header in ...
Nitesh Shriwash's user avatar
1 vote

How can to validate the presence of a certain type of cells in a single cell dataset?

I think the typical way to do this would be to identify a small number of marker genes whose presence and absence is specific for that cell type.
swbarnes2's user avatar
  • 1,812

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