Comments (2)
LuyiTian
commented on June 19, 2024
the annotation and relevant metadata is stored in colData(SCE_object_you_downloaded). let me know if you have any questions.
You can get the DE genes from bulk sample either from our previous study: "RNA-seq mixology: Designing realistic control experiments to compare protocols and analysis methods" (bulk but not the same batch of cells, grown at different time), or from the 90 cell control dataset (the same cells but not really bulk). And these DE genes can be used as ground truth for comparison.
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AlemuTA
commented on June 19, 2024
Thanks for the quick response. I downloaded the data from the GEO database, and I did not find a SingleCellExperment object to extract those meta data. I think I need to download the data again from this GitHub repository. Thanks again.
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Related Issues (15)
- All the methods tested in the paper all limited in R language? HOT 1
- How to perform log transformation？ HOT 3
- some question about clustering HOT 5
- Question regarding 10x UMIs HOT 1
- Is the 10X data 3' or 5'? Which chemistry was used? HOT 1
- can't reproduce the results in the paper HOT 1
- Plans to make into ExperimentHub package? HOT 3
- Number of cells discrepancy HOT 1
- five cancer cell line 10x data barcode+UMI length
- mitochondrial RNA
- A query about theoretical total input of spike-ins HOT 2
- Fix encoding(?) of the *_call.R scripts in script/clustering/Clustering_Algorithms HOT 1
- Rdata file contains variables with unclear names HOT 1
- Loading the data from Python HOT 2
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