Discussions

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  Different result everytime I run snap.tl.spectral

  MathildaStigenberg asked Oct 29, 2025 in Q&A · Unanswered

  

  

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  how to call snapatac2.ex.export_bigwig on cell indices directly?

  mkarikom asked Oct 3, 2025 in Q&A · Closed · Unanswered

  

  

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  How to address hdf5 latency and spawn errors when loading fragments in torch?

  mkarikom asked Oct 3, 2025 in Q&A · Unanswered

  

  

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  How to efficiently produce a 'pseudobulk level' track, where the subset is O(100k cells)?

  mkarikom asked Sep 6, 2025 in Q&A · Unanswered

  

  

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  Notes on feature selection

  research 🔬 more research needed

  kaizhang started Mar 14, 2023 in Ideas

  

  

  

  

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  Welcome to SnapATAC2 Discussions!

  kaizhang announced Mar 1, 2022 in Announcements

  

  

  

  

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  Suggestions on discriminating mitosis cells (proliferative cells) from non-proliferative cells by snapatacv2.

  wangmeijiao announced Mar 12, 2025 in Announcements

  

  

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  pp.import_data()

  pass-c started Aug 21, 2024 in General

  

  

  

  

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  Parallelisation using make_peak_matrix

  newtonharry started Oct 26, 2024 in General

  

  

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  Quantification of pseudo-bulked signal at cluster specific peaks from snap.tl.merge_peaks function

  skpeterson asked Oct 10, 2024 in Q&A · Closed · Unanswered

  

  

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  Understanding peak calling on whole dataset (piror to cluster identification)

  newtonharry started Oct 10, 2024 in General

  

  

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  How is frac_dup calculated?

  documentation 📖 Improvements or additions to documentation

  HaikuoLi asked Oct 9, 2024 in Q&A · Unanswered

  

  

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  Unsure on how to create variable-width bins using rebinning algorithm

  newtonharry started Oct 6, 2024 in General

  

  

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  Is there any code to handle hic data please? I didn't find it in tutorial. Thank you very much for your help!

  leowxvandy asked Aug 14, 2024 in Q&A · Unanswered

  

  

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  What counting method was using in v2.2.0?

  newtonharry started Aug 23, 2024 in General

  

  

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  Integration with SCENICplus

  TingTingShao announced Mar 16, 2024 in Announcements · Closed

  

  

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  Multi-Sample Pipeline and Cell Type Annotation

  florinwalter asked Aug 2, 2024 in Q&A · Unanswered

  

  

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  Differential motif enrichment

  CarstenKnutsen asked Oct 18, 2023 in Q&A · Answered

  

  

  

  

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  Why doesn't the KNN produce a connectivities in obsp?

  newtonharry started Jul 2, 2024 in General

  

  

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  Potential addition of Shared k-NN Graph function

  newtonharry started Jun 12, 2024 in Ideas

  

  

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  Usage principles on AnnDataSet

  dbrg77 started May 7, 2024 in General

  

  

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  Spectral embedding with mixed high/low depth nuclei samples

  wangmeijiao asked Apr 14, 2024 in Q&A · Unanswered

  

  

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  What is the input format to peak calling?

  adamklie started Apr 12, 2024 in General

  

  

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  snap.pp.mnc_correct groupby

  TingTingShao announced Apr 10, 2024 in Announcements

  

  

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  marker genes

  TingTingShao started Apr 2, 2024 in Ideas

  

  

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