Questions tagged [single-cell]
Questions about techniques in which the genetic material of a single cell is analysed individually
9 questions
5
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2
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Manually define clusters in Seurat and determine marker genes
I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I ...
- 2,578
12
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2
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determining doublets in single-cell RNA-seq
Doublets are a known problem with scRNA-seq experiments, where 2 or more cells are sometimes captured instead. To determine their presence, there are studies that mix multiple species (such as human ...
- 2,209
7
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3
answers
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Finding the optimal resolution parameter in Seurat's FindClusters function
In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
- 2,578
6
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2
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What are doublets in single cell RNA-seq data?
I am reading The Tabula Muris Consortium et al. (pp).
In some organs, cells with more than 2 million reads were also excluded as a conservative measure to avoid doublets.
How exactly is a “doublet”...
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5
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1
answer
624
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Single-cell RNA sequencing (scRNA-seq): filtering cells by transcript counts, how to choose cutoffs?
I am running a notebook with example for the MAGIC algorithm.
In the data preprocessing step, a filtering operation is required to filter out cells with a small count of transcripts.
My question is ...
- 1,823
5
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1
answer
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How to compute the chance of failing to detect a gene given the detection limit of a protocol
In Shapiro et al., when discussing about loss of molecules as source of error in single-cell sequencing, it is written that:
Another source of error is losses, which can be severe. The detection ...
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2
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1
answer
4k
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Cellranger aggr and Seurat merge difference?
I have multiple libraries of 10x Chromium single-cell RNA-seq data, which I'd like to combine. One option is using cellranger aggr which by default does a depth ...
- 2,644
2
votes
0
answers
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shiny app for single cell cluster export issue
I'm trying to create a shiny app for single cell data visualization and then label cells with genes till this step it works, the final step when I try to export cluster it is not exporting the desired ...
- 207
0
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1
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699
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Stacked barplot for single cell analysis
I want to create a stacked bar-graph with different cell cycles for each cell type within each condition. I have uploaded the file for it. Don't know how to go about it as now I have another condition ...
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