CARD

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Imputation expression levels in plot

3

Afternoon, thanks very much for providing CARD to the community, its been very helpful. I had one question regarding the imputation process as I am seeing some strange behaviors for...

jebard

Put CARD on Bioconductor

4

Hi there, Thank you for the great package! Could you please put it on Bioconductor, so that we could add it to the online book [Best Practices ST](https://lmweber.org/BestPracticesST/). Sincerely, Estella

estellad

Rotate CARD plots?

2

Hi there! Thanks for making and documenting such a nice package! Is there anyway you can rotate the spatial plots? Using the function copied below, I've been able to rotate...

hcjarnagin

Error in norm_cords$x - min(norm_cords$x) : non-numeric argument to binary operator

1

@YingMa0107 @YMalab I would greatly appreciate your help with this error: > # Run CARD deconvolution > CARD_obj = CARD_deconvolution(CARD_object = CARD_obj) ## create reference matrix from scRNASeq... ## Select...

krigia

Hi YMa-lab, I would really like to use your CARD_SCMapping function but every time I try to use it I run into this error. Error in data.frame(..., check.names = FALSE)...

lindsdudley

@YingMa0107 @YMalab I am getting the following error **_QC on scRNASeq dataset! ... ## QC on spatially-resolved dataset! ... Error: There are no common gene names in spatial count data...

krigia

sc and spatial count Matrix are correctly formatted but createCARDObject function returns error

2

@YingMa0107 @YMalab I have exported tha RNA counts for both scRNA-seq and spatial data as dgCMatrix. **str(scRNA_seq_counts) Formal class 'dgCMatrix' [package "Matrix"] with 6 slots ..@ i : int [1:37279034]...

krigia

How to add CARD result to Seurat object

2

Hi developer, Thanks for developing such amazing package for ST analysis. After deconvolution by CARD, how to add the results of CARD object to Seurat data for downstream analysis ?...

GouQiao

How to view informative genes for each cell type

2

Excellent work! I noticed that CARD requires the selection of informative genes for each cell type before proceeding with deconvolution. Therefore, I would like to know which genes are identified...

ghost

Multiple slices

1

Hi, I have multiple slices from 6 patients. For ST data, I divided them into 3 groups (2 sample for each group). And I also integrate scRNA-seq by groups. For...

GouQiao