GLUE
GLUE copied to clipboard
gao-lab
Graph-linked unified embedding for single-cell multi-omics data integration
Hi I am following pipeline from the GLUE publication to get the regulatory inference. In that attempt, I am at /GLUE/tree/master/experiments/RegInf)/s03_peak_gene_validation.py However I get following error ========================================================== Clustering metacells... ---------------------------------------------------------------------------...
Thank you for developing such a great tool! I'm working on integrating single cell and spatial transcriptomic data using GLUE. Because they have same var_name(gene name), it is confusing when...
Hi, I have been able to successfully use GLUE to integrate un-paired scRNAseq and scATACseq data. I was wondering if you have any pointers on using GULE to construct the...
See https://github.com/gao-lab/GLUE/blob/e20518b0ae7b39d47244087b825511e5c84f9b7e/scglue/data.py#L609 for the line from which `integration_consistency` makes this requirement. I am wondering why this is the case? I have floating point data I am trying to integrate.
Hi, thank you for your excellent tools! Recently, our collaborator generated a series of 10X multiome datasets, and we hope to use GLUE to our paired datasets. I found the...
If subsetting ~500 cells for both RNA and ATAC, in the training tutorial ```python rna = rna[rna.obs_names.isin(rna.obs_names[:500]),:].copy() atac = atac[atac.obs_names.isin(atac.obs_names[:500]),:].copy() print(rna.shape, atac.shape) ``` I get the following error (below) when...
Thanks for developing a nice tool! I used glue to integrate scRNA-seq and scATAC-seq datasets from multiple samples. I want to get clustering results covering both modalities in the umap...
Dear Authors, Hi all, I have added functions to implement the functions of integrating gene expression information and protein information from CITE-seq data. I have offered two options to model...
Does LSI require all peaks for optimal results, especially when dealing with ultra-scale datasets?
Hello, I currently have scATAC data with approximately 3.43 million cells and around 160,000 peaks. When I attempt LSI dimensionality reduction using all peaks, it takes an incredibly long time...
Hi, I am running GLUE -> experiments -> TripleOmics and I got the following error in file `e01_inmf_nbconvert.log`. ``` [NbConvertApp] WARNING | Config option `kernel_spec_manager_class` not recognized by `NbConvertApp`. [NbConvertApp]...
