Discussions

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  Ability to add matrices for multi-modal analysis

  connorrogerson started Jan 19, 2026 in Feature Requests

  

  

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  repalce matrix in ArchR

  qi825 started Sep 15, 2022 in General

  

  

  

  

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  Generate Releases and version more frequently

  mfansler started Oct 11, 2024 in Feature Requests

  

  

  

  

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  Issues with custom genome and GeneScoreMatrix creation in ArchR

  hayatkhanndsu started Dec 21, 2025 in Feature Requests

  

  

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  Integrating multiomic data (CITE-Seq + ATAC-seq)

  markphillippebworth started May 6, 2021 in Feature Requests

  

  

  

  

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  plotGroups HOW TO ORDER CLUSTER

  A-legac45 asked Apr 23, 2025 in Questions / Documentation · Unanswered

  

  

  

  

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  Iterative Peak Overlap normalization and usage

  plbngl asked Sep 1, 2025 in Questions / Documentation · Unanswered

  

  

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  Question about setting maxReplicates in addGroupCoverages()

  Captain-Pam asked Aug 22, 2025 in Questions / Documentation · Unanswered

  

  

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  An issue in addGeneIntegrationMatrix

  lzh-fugwaa asked Aug 22, 2025 in Questions / Documentation · Unanswered

  

  

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  Uneven representation of conditions in Peaks to Gene Heatmap

  cassidmm asked Jul 29, 2025 in Questions / Documentation · Unanswered

  

  

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  co-accessibility analysis

  superSXB asked Jul 24, 2025 in Questions / Documentation · Unanswered

  

  

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  simpleError in allLSI[cn, , drop = FALSE]: subscript out of bounds

  wshands started Jul 23, 2021 in General

  

  

  

  

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  ArchR with Windows: Space in Username causes issues after creating arrowfiles.

  Tomoliverberry asked Jul 13, 2021 in Questions / Documentation · Unanswered

  

  

  

  

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  problem with peak to genes

  A-legac45 asked May 20, 2025 in Questions / Documentation · Unanswered

  

  

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  Integrating freemuxlet results?

  leetde asked Apr 24, 2025 in Questions / Documentation · Unanswered

  

  

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  Monocle trajevtory is not running in my hand

  A-legac45 asked Apr 23, 2025 in Questions / Documentation · Unanswered

  

  

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  Manually calculating overlapping cell aggregates

  jayypaul started Apr 21, 2025 in General

  

  

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  Could I get the enriched motif of peaks to a specific gene (The results of 'p2g')

  ChangliangWang asked Apr 23, 2021 in Questions / Documentation · Answered

  

  

  

  

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  Remove cellColData info

  NoemieL asked Mar 5, 2024 in Questions / Documentation · Unanswered

  

  

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  ArchR for single nuclei CUT&TAG

  GDS97NYC asked Apr 8, 2025 in Questions / Documentation · Unanswered

  

  

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  Contenerized ArchR for HPC

  drowsygoat started Aug 5, 2024 in General

  

  

  

  

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  Various package issues with bioconda r-archr 1.0.3 release

  Pirhhot started Feb 28, 2025 in General

  

  

  

  

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  State of Issue #582

  Pirhhot started Apr 7, 2025 in Feature Requests

  

  

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  General questions about interpretation of differential peaks

  Pirhhot asked Apr 4, 2025 in Questions / Documentation · Unanswered

  

  

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  Can Macs3 be used to call peaks?

  amderogatis asked Jan 9, 2024 in Questions / Documentation · Unanswered

  

  

  

  

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