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Hi,
Thanks for developing such an excellent tool for single-cell genomics. I am wondering whether you could provide the processing pipeline for Easysci-ATAC-seq.
Thanks.
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Forgot to return a response in an endpoint and realized I couldn't cancel the request from ATAC; the only way I was able to was by closing the app and rerunning atac.
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Hi TREASMO team,
paper looked really cool! So I wanted to try and run on some of my own data and the code provided:
rna = ad.read_h5ad('data/HSPC_Muon_RNA.h5ad')
atac = ad.read_h5ad('data/HSPC_Muon…
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Hi! I ran into this error:
“Error in checkGrep(grep(".A.txt", files)) :
Improper folder specification; file missing / extra file present. See documentation
Calls: importMito -> checkGrep
E…
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Hello,
I used LINGER 1.67 version. I had errors showing "raise KeyError(f"{not_found} not in index")" when I run `LL_net.cell_type_specific_TF_RE_binding(GRNdir,adata_RNA,adata_ATAC,genome,celltype…
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Thank you very much for sharing. I found that some data was not sorted during the reproduction process. How do you handle the sorting of these data such as BMMC data how to sort?Can you provide a tuto…
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Hi!
I was following the tutorial for integrating scRNA-seq data and scATAC-seq data using the dataset provided. However, I get the following error when I run the step: atac = tfl.findNeighbors(adat…
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Congratulations on the wonderful-looking update on VIA.
This is my first time trying to use VIA (or StaVia), and it seems like the tutorial for [scATAC-seq Hematopoiesis] link is not working corre…
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I have 3 replicates of spatial RNA+ATAC multiomics data, can SpatialGlue integrate them together? Or I must cluster each slice individually?
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Hi,
I have some some bulk ATAC and RNA seq in which I wanted to identify some DORCs. Is it possible to use the dorc function in this kind os data (ie importing my bulk rds into the objects)? Of cour…