Discussions

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  Error Report: seqinfo error with custom genome in Signac/Seurat

  hayatkhanndsu started Dec 24, 2025 in General

  

  

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  How to analyze a subset from multiome (ATAC + RNA-seq) data

  LuciaJim asked Nov 21, 2025 in Q&A · Unanswered

  

  

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  How to handle redundant motif in enrichment results (AP-1 family)

  syeong8 asked Dec 2, 2025 in Q&A · Unanswered

  

  

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  Target gene of Transcription factor(TF)

  summer-tao started Apr 19, 2021 in Ideas

  

  

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  FractionCountsInRegion() returns values > 1

  Almr95 asked Oct 14, 2025 in Q&A · Unanswered

  

  

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  Request for an example vignette for integrating multimodal datasets

  wudustan started Sep 22, 2025 in Ideas

  

  

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  Custom annotation - help to bypass/change it for GO, TF, etc-ATAC-related analysis

  NadiaEdel asked Sep 2, 2025 in Q&A · Unanswered

  

  

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  MACS3 callpeak vs HMMRATAC

  DineshRavindraRaju asked Aug 27, 2025 in Q&A · Unanswered

  

  

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  Missing per_barcode_metrics.csv in dataset

  athefj asked Aug 22, 2025 in Q&A · Unanswered

  

  

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  Creating fragment object for common peak set (multiome 10x)

  NadiaEdel started Aug 4, 2025 in General

  

  

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  Signac tutorial counts$Peaks includes extra contigs not in annotation file

  arajeevan asked Aug 18, 2025 in Q&A · Unanswered

  

  

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  Calling peaks with group.by or creating a common peak set?

  klgoss asked Sep 13, 2023 in Q&A · Answered

  

  

  

  

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  Calculate QC metrics (Nucleosome signal, TSS enrichment, FRiP, etc) before or after merging multiple datasets?

  rgdani asked Jul 24, 2025 in Q&A · Unanswered

  

  

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  co-accessibility analysis

  superSXB asked Jul 24, 2025 in Q&A · Unanswered

  

  

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  Integrating multimodal data from multiple samples

  bapoorva asked Jul 21, 2025 in Q&A · Unanswered

  

  

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  Inclusion of extra-species motifs in RunChromVAR()

  sarah-chapin asked Jun 30, 2025 in Q&A · Unanswered

  

  

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  Difficulty removing depth correlation in clustering

  APuchkina asked Jul 4, 2025 in Q&A · Unanswered

  

  

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  integration of several multiome datasets

  documentation Documentation help

  mengm5 asked Oct 10, 2024 in Q&A · Unanswered

  

  

  

  

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  any plans on moving to MACS3?

  brianlamere started Jun 23, 2025 in General

  

  

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  Issue with LinkPeaks() — Assigning peaks to RNA object hangs for one tissue-specific subset

  CuilingHe asked Jun 24, 2025 in Q&A · Unanswered

  

  

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  Can I use RPCA in FindTransferAnchors between RNA and ATAC?

  plbngl asked May 6, 2025 in Q&A · Answered

  

  

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  Inquiry Regarding Absence of Blacklist Regions for Sus scrofa in ATAC-seq Analysis

  documentation Documentation help

  tianxuekai asked May 23, 2025 in Q&A · Unanswered

  

  

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  Inconsistent Signal in CoveragePlot Compared to DE and DA Results for Mki67

  Jyng321 started May 5, 2025 in General

  

  

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  data processing that were not produced by 10X genomics

  dahun73 asked Apr 11, 2025 in Q&A · Unanswered

  

  

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  Strange behavior with scATAC integration using Harmony

  jeremymsimon asked Mar 14, 2024 in Q&A · Unanswered

  

  

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