cTPnet

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Hi, May I ask if this tool can be used for integrative data? the cell embeddings would be used to visualize the integrative data, so I used the code as...

vgettaa

Hi, thanks for this tool. I wonder if the training data can be downloaded somewhere? ```python X_list=['../data/PBMC_Stoeckius/PBMC_tl.csv','../data/CBMC_Stoeckius/CBMC_tl.csv','../data/BMMC_Stuart/GSE128639_RNA_counts_denoised_filt.csv','../data/PBMC_Ye_Pre/p1_illumina_raw_filtered_RNA_denoised.csv','../data/PBMC_Ye_Pre/p2_illumina_raw_filtered_RNA_denoised.csv'] y_list=['../data/PBMC_Stoeckius/GSE100866_PBMC_vs_flow_10X-ADT_umi.csv','../data/CBMC_Stoeckius/GSE100866_CBMC_8K_13AB_10X-ADT_umi.csv','../data/BMMC_Stuart/GSE128639_citeseq_adt_counts.tsv','../data/PBMC_Ye_Pre/p1_illumina_raw_filtered_Antibody.csv','../data/PBMC_Ye_Pre/p2_illumina_raw_filtered_Antibody.csv'] header_list=['PBMC_Stoeckius','CBMC_Stoeckius','BMMC_Stuart','PBMC_Ye_Pre_p1','PBMC_Ye_Pre_p2'] ``` Thanks!

crazyhottommy

How to plot the correlation?

3

Hello. I would like to apply your amazing tool to my current scRNA-seq research projects. May I ask where I can find the code you used to generate Fig 1B...

levinhein

Mouse data

1

Hi, Is it possible to use this tool with mouse data? if not, Is there a way to train our own models? Thanks for your time.

torgheh

I have some questions about REAP-PBMC dataset

1

Hi dear Zilu, Thanks for developing a very useful tool! When I follow the methods on the original paper to perform quality control on REAP-PBMC dataset, I can't get the...

CCNU-LCY

How to define the internal layers related to informative for cell type, cell state, and common processes such as cell cycle?

1

gancao

ModuleNotFoundError: No module named 'ctpnet'

13

Hi, When I went through the demo analysis and tried to import the pretrained model, I got this error message below: model_file_path="C:/Users/User/Documents/cTPnet_weight_24" data_type='Seurat3' demo = CreateSeuratObject(demo_data) demo = cTPnet(demo,data_type,model_file_path) >...

amber4mint