SnapATAC2
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kaizhang
Single-cell epigenomics analysis tools
Hi and thanks for developing this very useful tool! when i tried to use snapatac2.tl.add_cor_scores(network, peak_mat= data) it gives me error of "'NoneType' object has no attribute 'obs_names'" data:Anndata scATAC...
This PR is an attempt to fix the CI error encountered in `.github/workflows/test_python.yml`. I **haven't** had a chance to actually test that this works so feel free to modify or...
Hi Kai, I have an anndata.AnnData, I can generate the snapatac2.AnnData as followed ``` # ann is an anndata.AnnData sa2ann = snapatac2.AnnData(filename = "tmp.h5ad", X = ann.X) ``` When I...
this is being run within the recommended container for `snap.pl.umap(data, color='leiden', interactive=False, height=500)` ``` --------------------------------------------------------------------------- KeyError Traceback (most recent call last) Cell In[17], line 1 ----> 1 snap.pl.umap(data, color='leiden', interactive=False,...
Hi, So I'm currently working on a multi-sample pipeline and I've followed your tutorial. I currently have to rename barcodes such that they're the same across snATAC-seq and snRNA-seq data....
Hi Kai, I found that the description of read_mtx is not clear. 1. obs_names: File that stores the observation names. - obs_name_file would be better, otherwise, it's hard to know...
The recommended interactive container built nicely on ubuntu 22.04 but attempt to run first chunk of annotation.ipynb led to ``` 2024-02-13 14:15:57 - INFO - generated new fontManager --------------------------------------------------------------------------- AttributeError...
Hi, first of all thanks a lot for this great tool! I was wondering if it would be possible to have the make fragment files function from bam files also...
Hi, Could I please ask if there is one way to color the cells with openness of a certain region. For example, if I found a regions is very interesting,...
I would like to inform you that I have pushed the SnapATAC2 v2.6.0-recommend-interactive-py3.11 Docker image to Docker Hub. The image can be found at: [[1316057503/napatac2:v2.6.0-recommend-interactive-py3.11]](https://hub.docker.com/repository/docker/1316057503/napatac2/general) Thank you for developing such...
