Discussions

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  Cells in the fragment object disappear after integration

  AyeGonzalezMontoro asked Dec 19, 2024 in Q&A · Unanswered

  

  

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  How do I create a BSGenome for Gallus gallus from ENSEMBL?

  pcantalupo started Dec 10, 2024 in General

  

  

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  Opinions on scMultiome pipeline

  kryptonitecircuit2002 asked Dec 10, 2024 in Q&A · Unanswered

  

  

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  Discrepancy in TSS enrichment score between cellranger and Signac: am I using the wrong annotation?

  MarkoBarovic asked Apr 9, 2024 in Q&A · Unanswered

  

  

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  Integrating joint snATAC/RNA-seq experiments

  cristanchoa asked Feb 10, 2021 in Q&A · Answered

  

  

  

  

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  How do I integrate snATAC-seq data from different samples?

  SaharBJ asked Nov 26, 2024 in Q&A · Unanswered

  

  

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  How do I find the processed object from the multiomic pbmc tutorial?

  SaharBJ asked Nov 26, 2024 in Q&A · Unanswered

  

  

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  Issues with custom annotation

  kryptonitecircuit2002 asked Nov 25, 2024 in Q&A · 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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  Analyzing PBMC scATAC-seq Using Signac Error

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

  

  

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  Filtering nucleosomal fragments

  leandro-ventimiglia started Nov 7, 2024 in General

  

  

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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 · Answered

  

  

  

  

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  CoveragePlot plotting additional ranges as multiple separate tracks

  jenellewallace asked Aug 20, 2024 in Q&A · Answered

  

  

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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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  integration of several multiome datasets

  documentation Documentation help

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

  

  

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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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  Reproducing CoveragePlot results during differential peak analysis

  documentation Documentation help

  si3 asked Oct 4, 2024 in Q&A · 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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  How sequencing depth impacts the number of DARs?

  documentation Documentation help

  sshanyiiii asked Sep 27, 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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