STitch3D

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unsupported operand type error in preprocessing

3

Dear professor, I am getting this TypeError: unsupported operand type(s) for &: 'str' and 'str' error in the function preprocessing in utils.py on the line 205. I tought that genes_shared...

lillyzhan

DLPFC dataset

4

Dear Professor, Thanks for your explanation and patience! I want to know how can I find the DLPFC dataset in the tutorial: anno_df = pd.read_csv('./data/spatialLIBD/barcode_level_layer_map.tsv', sep='\t', header=None) adata_st1 = sc.read_visium(path="./data/spatialLIBD/%d"...

cristalliao

Compare with other deconvolution methods

2

Dear Professor, I have a question about comparing it with other deconvolution methods. In the paper, there is one figure about the Estimated proportions of cell types obtained from STitch3D...

cristalliao

Human heart dataset comparison with other methods

4

Dear Professor, I am very impressed with the STitch3D technology. I want to know how to do the model evaluation with different methods. I think the data processing part is...

cristalliao

Problems in loading the human heart original dataset into R

3

Dear Professor, I have encountered some problems in loading the human heart dataset into R. Could you please help me to check what the problem is? Firstly, I read the...

cristalliao

Where can I find the single cell RNAseq count data for each slice?

2

Dear Professor, I have a question how can I use the 6.5 PCW human embryonic heart dataset in another Model? For example, I want to use the CARD technique, it...

cristalliao

How can I find cell type for Example 2 dataset?

1

Hi Professor, I have a question about the cell type, I want to know how can I find the cell type for the Example 2 dataset. For example, we have...

cristalliao

Where is the code for Supplementary Information?

2

Dear Professor, I want to know where is the code for Supplementary Information. Since there are lots of graphs and tables in the paper and the supplementary Information, where can...

cristalliao

Can't find seurat_clust_1620.txt

1

Dear professor: I cannot find this txt file "seurat_clust_1620.txt" in example 3 "Run STitch3D on the Drosophila embryo dataset" clust = pd.read_csv("./data/Calderon_2022/seurat_clust_1620.txt", sep=" ") Could you tell me where I...

Peter-Fung

Application on mouse hypothalamic preoptic region MERFISH data

1

Dear Professor, I saw that you mentioned the results on the MERFISH dataset in the supplementary materials. I wonder if you could provide the code applied to the MERFISH dataset?...

lvyanzhe