Tangram

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Problems about ploting

2

Hi, I found an error from the tutorial:  Moreover, the final output with deconvolution result does not display in my jupyter notebook, is it normal? Thanks a lot. 

HelloWorldLTY

Option "enforce gene lowercase"

1

Hi, It's great that you added the option of "gene_to_lowercase=False" in tg.pp.adatas, so the gene names don't get automatically converted to lower case. Can you also add this option to...

yinan-wan0

Cannot find correspondence of the input data

1

Hi, Thank you for providing the detailed code for use. I have noticed a discrepancy between the number of spots mentioned in the MERFISH tutorial and the paper. I assume...

cindyway

Question about acceptable AUC, improving AUC

1

Hi Tangram Team, I've been working with tangram-sc and am seeking advice on improving the AUC (Area Under the Curve) of my models for 10x visium. - Could you provide...

boyangzhang1993

Interpretation of tangram_ct_pred

2

Greetings, I am using Tangram to annotate my spatial data (10X) using single cell data. I would like to better understand the output of project_cell_annotations(). It says “INFO:root:spatial prediction dataframe...

abhishekmaj08

Unexpected behaviour

1

Hi, Thanks for making such a easy-to-use and well documented package! I was using it and noticed that my adata object got modified and essentially broke my pipeline downstream. Please,...

dbdimitrov

Possible to use multiple single cell datasets in Tangram?

3

Thanks for developing Tangram, and it is very much appreciated. Is it possible to use multiple single-cell datasets, such as merged two datasets, for predictions? Would you recommend making predictions...

boyangzhang1993

Some questions about best practices

1

Hello Tangram developers, I'd like to ask a question that might help me clarify whether Tangram is a good choice for my large visium dataset. So, it seems to me...

Dillon214

Can we have an API as batch size for the integration method?

3

Hi, My dataset is very large, which cannot be handled by tangram, so I wonder if it is possible to have a key or api known as batch size to...

HelloWorldLTY

Projecting spatial annotations to single cell

2

Hello! I'm currently working with the MOSTA dataset (Mouse Stereo-seq), and I have two questions: * Do you recommend using specific parameters to work with this kind of data? *...

tvegawaichman