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Answer: `emptyDrops()` calling 'too many' non-empty droplets
by
Aaron Lun
★
27k
Perhaps there is something wonky with the TCR sequences that exclude them from the barcodes with below 100 counts. Maybe TCR sequences are …
Answer: how to do downstram analysis to cells which are subsetted after MNN batch-correc
by
Aaron Lun
★
27k
In this case, you can just replace `denoisePCA` in the example with the various MNN steps. So:
```
# NOTE: not tested!
sce.sub <- sce[…
Answer: how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more rea
by
Aaron Lun
★
27k
It is, in general, difficult to interpret the `reconstructed` assay, as batch correction is not guaranteed to do "sensible" things to the p…
Comment: How to get started with DeseqDataSet import using CSV? Is it necessary to have C
by
ATpoint
★
1.4k
Please provide an example of that sheet (at best after reading into R and then shared via `dput()`) if you are seeking help. In general the…
Comment: Which is the best type of data for correlation or survival analysis
by
Yang Shi
•
0
Hi ATpoint, thanks for your reply and show me the thread. But there are still some questions:
(1) **dds <- estimateSizeFactors(dds); ntd <…
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