SnapATAC2
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kaizhang
Single-cell epigenomics analysis tools
data = snap.read_dataset("combined.h5ads") data AnnDataSet object with n_obs x n_vars = 277377 x 526765 backed at 'combined.h5ads' obs: 'sample', 'leiden' var: 'count', 'selected' uns: 'spectral_eigenvalue', 'AnnDataSet', 'reference_sequences' obsm: 'X_spectral_mnn', 'X_spectral',...
Hi Kai, I add three parameters for peak calling. 1. On bed graph generation: - SPMR and store_bdg, I open the two parameters since we notice that MACS2/3 can generate...
Hi Kai, I have several AnnData created directly from fragment files. If I did not add any matrix to AnnData's X, and combine them into AnnDataSet (this step is OK)....
Hello. Thank you for this package. I'm doing an integration analysis using more than 40 scATAC samples. However, I do not have scRNA data from the same cells. I tried...
The tutorial mentions use of a RNA multiome file[(`reference = snap.read(snap.datasets.pbmc10k_multiome(), backed=None`)] for annotation of clusters in scATAC dataset (https://kzhang.org/SnapATAC2/tutorials/annotation.html).
Hi Kai, thank you so much for this wonderful tool! Just one question, Can I use snapATAC tutorial for snapATAC2? As the snapATAC2 doesn't have tutorials for downstream analysis.
Hello @kaizhang and thank you for this great software. I am curious if you have any vignettes available that walk through some of the downstream functions like `tl.link_tf_to_gene` or `tl.add_tf_binding`...
Hello, Thanks for the great package! I am trying to extract the fragment count matrix to implement with the following notebook: https://github.com/aertslab/pycisTopic/blob/old/notebooks/Toy_melanoma-RTD.ipynb However, I cannot see where to extract the...
Hi Kai, Is that possible we can provide more parameters to simulate the behavior of bamCovrage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html I think it might be not our goal to support all the parameters...