SCALE
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jsxlei
Single-cell ATAC-seq analysis via Latent feature Extraction
The link to the data availability in the tutorial is no longer accessible. Would it be possible to provide an updated link or alternative access to the data? thanks
Hi, I have reproduced using the data mentioned in the article and although both the tSNE plot and the UMAP plot show that they can separate the cell taxa correctly,...
Hi, I am trying to apply this to the Pancancer dataset (Sequencing-based gene expression) from the ICGC portal but the result was no good. The data points entangle with each...
Dear Lei, When I ran SCALE, I can't get the output document of "cluster_assignments.txt" . So I want to know how to get the clustering results "cluster_assignments.txt". Thanks.
Hi, I met some problems when create the environment. After I run `setup.py install', it shows the numpy version is not correct "error: numpy 1.22.1 is installed but numpy=1.18 is...
Dear Lei, I recently encountered a problem regarding the imputation. I used SCALE already some time ago and I remember I could get data about imputation using the --binary flag...
I tried to use GPU to run SCALE by this commond `SCALE.py -d a.txt -k 20 --binary --gpu 1` But I got this error: ``` Traceback (most recent call last):...
Hi, I was wondering for your original publication, how large the input dimension (number of peaks) the SCALE model can accommodate. Sometimes the scATACseq give us over 100k features/peaks, I...
Hi, SCALE is a very interesting and useful tool. But I have a question about the calculation of ELBO. Why gamma=q(c|x)=p(c|z) is used to calculate ELBO instead of q(z,c|x)? Does...
Thanks for developing this tool! I'm hoping to run SCALE on scATAC data and output the model with best performance. Right now it seems early stopping is not working, would...
