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 ...
- 119
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 ...
- 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 ...
- 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 ...
- 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 ...
- 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. ...
- 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__♦
- 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
...
- 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:
...
- 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
- 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__♦
- 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__♦
- 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__♦
- 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__♦
- 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 ...
- 500
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 ...
- 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....
- 11
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 ...
- 193
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.
- 1,812
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