Discussions

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  SortIdents not in v1.14.0?

  sagrimm0 asked Nov 18, 2024 in Q&A · Unanswered

  

  

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  If I only have the 10x matrix files for scATAC and don't have the fragments file, can I use Signac to analyze the scATAC data? How should I do it?

  szbssg asked Aug 6, 2024 in Q&A · Unanswered

  

  

  

  

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  Filtering nucleosomal fragments

  leandro-ventimiglia started Nov 7, 2024 in General

  

  

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  Analyzing PBMC scATAC-seq Using Signac Error

  sohumsharma484 asked Oct 25, 2024 in Q&A · Unanswered

  

  

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  CoveragePlot plotting additional ranges as multiple separate tracks

  jenellewallace started Aug 20, 2024 in General

  

  

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  Does CoveragePlot scale by the number of cells in a category

  documentation Documentation help

  Connorr0 asked Jun 3, 2021 in Q&A · Answered

  

  

  

  

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  Any way to de-noise footprint plots in Signac?

  ptk1601 asked Oct 8, 2024 in Q&A · Closed · Unanswered

  

  

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  Peak links disappearing when I specify genes?

  ptk1601 asked Oct 1, 2024 in Q&A · Closed · Unanswered

  

  

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  Integrating 10x sc-multiomics (scATAC )across species

  JianiC asked Sep 29, 2024 in Q&A · Unanswered

  

  

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  Whether to use FindAlllMarkers features or AverageExpression features for displaying over-represented motif based on chromvar data

  revolvefire asked Sep 19, 2024 in Q&A · Unanswered

  

  

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  the prediction.score.max was low after joint scRNAseq and scATACseq

  Shuresearcher asked Sep 17, 2024 in Q&A · Unanswered

  

  

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  Recommendation to regress out confounding variables in scatac dataset?

  ejc043 asked Aug 28, 2024 in Q&A · Unanswered

  

  

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  It's possible to impute/enhance peak signals for scATAC-seq dataset by signac ?

  PeggySze started Mar 16, 2022 in General

  

  

  

  

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  Cannot add ATAC assay to Seurat Object? Following "Joint RNA and ATAC analysis: 10x multiomic" Vignette.

  sohkhar started Aug 23, 2024 in General · Closed

  

  

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  Advice on trisomy data

  mpt004 asked Aug 12, 2024 in Q&A · Unanswered

  

  

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  SNP infomation

  enhancement New feature or request

  nhu-github asked Aug 11, 2024 in Q&A · Unanswered

  

  

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  Significant Discrepancy in Peak Counts Between Cell Ranger ATAC and Signac Peak Calling

  mano2991 started Aug 10, 2024 in General

  

  

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  Integrating ATAC-seq data from multiple species with a consensus peak set

  jenellewallace asked Jul 30, 2024 in Q&A · Unanswered

  

  

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  GeneActivity on pseudo-bulk data

  enhancement New feature or request

  jgarces02 asked Jul 11, 2024 in Q&A · Unanswered

  

  

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  TSSEnrichment error

  hjyshane asked Jul 10, 2024 in Q&A · Unanswered

  

  

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  QC about TSS.enrichment and nucleosome_signal

  documentation Documentation help

  siqi-zZ asked Jul 9, 2024 in Q&A · Answered

  

  

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  10X multiome subsetting cancer cell line with blacklist_ratio ~ 1 for both hg38_blacklist and hg38_blacklist_unified

  methornton asked Jul 9, 2024 in Q&A · Unanswered

  

  

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  TSS enrichment issue

  hjyshane asked Jul 9, 2024 in Q&A · Unanswered

  

  

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  doublets removeal

  documentation Documentation help

  ZengMuo asked Jul 3, 2024 in Q&A · Unanswered

  

  

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  Question for obtaining nucleosome free region

  documentation Documentation help

  dbswls0322 asked Jul 9, 2024 in Q&A · Unanswered

  

  

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