Tangram

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Interpreting project_genes

4

Hi, Thank you for all your help in the running tangram! For interpreting the `project_genes` results, I noticed that it returns a "spot-by-gene AnnData containing spatial gene expression from the...

kguion1

It would be super useful if you could add an option to `tg.plot_genes_sc()` and `tg.plot_cell_annotation_sc()` so that the tissue image is shown in black and white. The pink colour of...

simonmfr

Question about training score in reference dataset

1

Hello, I am followind the tutorial but using a single nucleus dataset as reference, and trying to map it to a visium sample. It seems I am finding a very...

rimelof

the coordinates are flipped

2

Hello, thank you for creating such a useful tool, I am very happy to use it in my data, but when I draw a graph with tg.plot_cell_annotation_sc, I find that...

Lena926

why enforce lowercase?

4

https://github.com/broadinstitute/Tangram/blob/3c87a25d49ad50b7f85ba68c67d31b46e38c3847/tangram/mapping_utils.py#L40-L41 think it'd be useful if this operation is optional.

giovp

Question about parallelizing over multiple GPUs

2

Hello! I don't have much experience using PyTorch, and I was wondering if Tangram could be easily modified to parallelize over multiple GPUs? I am trying to map onto a...

brianysoong

This implements `option 1` i.e. mapping NMF W*H on spatial data. @hejinhuang could you please review it?

anupriyatripathi

prior density

4

Hi, Thanks for you great work. Now I'm trying do perform tangram with squidpy. I am confused about the density_prior function. It's said in the help document: density_prior (str, ndarray...

wangjiawen2013

conda package conflict

1

Hello, I have cloned the repo and am running: `conda env create -f environment.yml` But I get this error:  Not sure what to do besides install things one at...

jonathanperrie

Different celltype ratios of single cell data and spatial data

3

Hi, Thanks for sharing the Tangram. It is a very interesting work. I wonder can the tangram algorithm works well when the ratios of cell types of spatial data and...

cuicathy