Discussions

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  gene annotation for unpaired data

  ruohuchengxhe asked Apr 25, 2025 in Q&A · Unanswered

  

  

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  Non-binarization of matrix for non scATAC-seq data?

  simozhou started Apr 7, 2025 in Ideas

  

  

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  Questions about peak calling and data harmonization

  fstrijth asked Feb 11, 2025 in Q&A · Unanswered

  

  

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  how to subset cells on a pycisTopic object?

  Melody-cell started Nov 18, 2024 in General

  

  

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  what's the principle of the integration of snATAC-seq and scRNA-seq data during label transfer step?

  Melody-cell started Nov 22, 2024 in General

  

  

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  If I get a low TSS enrichment, how can I filter it effectively?

  Melody-cell asked Nov 16, 2024 in Q&A · Unanswered

  

  

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  Does the number of peaks in the accessbility matrix affect the results of pycisTopic?

  massonix asked Oct 31, 2024 in Q&A · Unanswered

  

  

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  Why psuedobulk then QC

  TingTingShao started Mar 20, 2024 in General

  

  

  

  

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  Conversion from snapatac2 to pycistopic

  lf96abc started Aug 15, 2024 in General

  

  

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  Guidance on topic model selection

  AmosFong1 asked Jul 23, 2024 in Q&A · Unanswered

  

  

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  get_gene_activity

  TingTingShao asked May 27, 2024 in Q&A · Unanswered

  

  

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  Start from the count matrix tutorial no longer available

  degrainger started May 21, 2024 in General · Closed

  

  

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  find_diff_features

  TingTingShao asked Apr 15, 2024 in Q&A · Closed · Answered

  

  

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  QC Based on Nucleosome Signal?

  salwanbutrus asked Mar 23, 2024 in Q&A · Closed · Unanswered

  

  

  

  

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  Issue when running run_cgs_models_mallet() prior to scenic+

  laurajohanne started Mar 26, 2024 in General

  

  

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  Performance optimisation request [PERFORMANCE]

  TingTingShao asked Mar 20, 2024 in Q&A · Unanswered

  

  

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  very low number of cells passed QC

  Aya-Balbaa asked Feb 21, 2024 in Q&A · Closed · Unanswered

  

  

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  Best number of topic always goes to maximum of the topics range

  simozhou asked Jan 23, 2024 in Q&A · Answered

  

  

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  normTop?

  dagarfield started Oct 27, 2023 in General

  

  

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  How to define "atac_anndata" in the toturial ??

  bitcometz asked Sep 27, 2023 in Q&A · Unanswered

  

  

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  Tutorial for scATAC, when you also have scRNA-seq data but not in multiomics

  MariaRosariaNucera asked Jul 21, 2023 in Q&A · Unanswered

  

  

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  Add umap into cisTopic object?

  zhangqc723 asked Aug 17, 2023 in Q&A · Answered

  

  

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  Sparcity resulting in empty DataFrames in the markers_dict object

  rkelly712 asked Dec 13, 2022 in Q&A · Unanswered

  

  

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