garnett

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Checking my markers for upcoming "Training my own classifier" steps

2

I have a cds object file for which I want to do single cell RNA seq analysis (make UMAP and identify cell types) on using monocle and garnett software, I...

techgirl2022

Run time to train new classifier

1

Hi, Thank you for creating the tool. I am trying to build new classifier using a total of 100 markers using a total of 5000 cells (train_cell_classifier). I wonder how...

lwtan90

Allow to extract assignment from all classification levels

4

Hi, The more I look at garnett, the more promising it seems, thanks for developing it! But currently it requires very detailed specification of cell type markers, which is not...

VPetukhov

hpliner

Gene X > Gene Y

hpliner

Put non-count data in CDS objects

8

Hi, I'm afraid this is more of a question than a bug report. Thus, I am deviating from the template. I haven't been able to find out how to load...

LuckyMD

Regeneration Classifier

4

Please provide the following info when submitting a new classifier: Species: Mouse Tissue/sample: Neuron Author(s): Hugo Kim Data source (if you generated the data, indicate yourself): myself Published? (if so...

neurohugo

Unable to download package

3

Sorry, when I tried to use this package, I found the command devtools:: install_ Github ("cole trapnell lab/garnett", ref="mono cle3") cannot install this package. The timeout is displayed. Then I...

xu15825503775

check_markers function using each cell as a different cell type

3

Hi, I am trying to check markers for a list and it seems like the cell type information is not being used for some reason. Total_nominated is close to the...

hd4git