Qirong Mao

Parameters of squidpy.gr.spatial_neighbors()

1

Dear Squidpy developers: I'm not quite sure some of the parameters in ```squidpy.gr.spatial_neighbors()``` function. I noticed that there are parameters of ```n_neighs``` and ```radius``` for the generic coordinates data, what's...

Do we need to normalization and scaling before calculating spatial autocorrelation?

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Hi Squidpy developers: I am looking for using squidpy to measure the spatial autocorrelation (like Moran's I ) for genes in spatial dataset. I was wondering if the result would...

Annotating cluster labels after cell segmentation on Visium

3

Hi, I had some questions about the cluster annotation after cell segmentation I tried to map the single-cell data to Visium and got the probability of the spatial location of...

Hi, thanks for developing FLAMES, very nice tool. One question about the transcript_count.csv.gz output, I got the result like this:  Where the transcript id name is quite weird, do...

Using single cell data from different sources as input

1

Hi, We are trying to use single-cell data from different sources as input for CARD to do the deconvolution. Since the input for CARD is raw counts. I was wondering...

Basis matrix is different for the same snRNA-seq but different spatial samples

2

Hi, thanks for presenting CARD. One question regarding the basis matrix construction, I've used the same snRNA-seq to deconvolute different spatial samples, but the gene list in the basis matrix...

Spatial LIANA x cell2cell analysis in R

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Thank you for developing the cell2cell pipeline. I am curious whether it's possible to perform spatial transcriptomics analysis using LIANA x cell2cell in R, given the challenges of interoperability between...

Memory exceeded when running single cell data alignment

23

 Hi, I tried running a task with a memory limit of 250GB, but it kept going over the limit. I'm thinking the problem might be related to how...