Issues

• [BUG] plotTSSEnrichment() crashes entire R‑session on native Windows

  bug
  GreenleafLab/ArchR#2332 · Filter by author Yong-rong opened on Aug 21, 2026
  1

• Hello, I encountered the error 'ERROR Found in .addGeneScoreMat TmpGS for' while using ArchR to create createArrowFiles

  bug
  GreenleafLab/ArchR#2327 · Filter by author wujian-njau opened on May 31, 2026
  1

• configure script fails quietly when calling "wget http...". Worked when changing to "wget https..."

  bug
  GreenleafLab/ArchR#2326 · Filter by author pvo93 opened on May 12, 2026
  4

• Batch correct by other algorithm

  bug
  GreenleafLab/ArchR#2324 · Filter by author songlyzz opened on Apr 3, 2026
  1

• subscript out of bounds error in addIterativeLSI on Ubuntu but works on Windows

  bug
  GreenleafLab/ArchR#2319 · Filter by author shaoxiong2588 opened on Jan 6, 2026
  2

• Why the cell numbers in ArchR project differed from the results from cellranger-atac

  bug
  GreenleafLab/ArchR#2318 · Filter by author CampingOnSeabed opened on Dec 25, 2025
  1

• error occurred in addReproduciblePeakSet

  bug
  GreenleafLab/ArchR#2316 · Filter by author YunjieLi22 opened on Dec 12, 2025
  1

• Error: addGroupCoverages

  bug
  GreenleafLab/ArchR#2315 · Filter by author zeyan-0717 opened on Dec 1, 2025
  1

• Iterative overlap for peak merging

  bug
  GreenleafLab/ArchR#2313 · Filter by author plbngl opened on Sep 16, 2025
  1

• Inconsistent results from pseudo-time heatmap and UMAP embedding of peaks

  bug
  GreenleafLab/ArchR#2306 · Filter by author callmeracle opened on Jun 30, 2025
  3

• Error in doubScores function

  bug
  GreenleafLab/ArchR#2305 · Filter by author SergioManzano10 opened on Jun 11, 2025
  2

• beyond boundries when using addMotifAnnotations

  bug
  GreenleafLab/ArchR#2304 · Filter by author xmliu01 opened on May 23, 2025
  1

• ArchR complains about nabor package not available even if nabor is loaded

  bug
  GreenleafLab/ArchR#2302 · Filter by author JackieMium opened on Apr 28, 2025
  1

• TRJECTORY analysis -< getMonocleTrajectories()

  bug
  GreenleafLab/ArchR#2297 · Filter by author A-legac45 opened on Apr 17, 2025
  1

• addArchRLogging(FALSE) Does not work

  bug
  GreenleafLab/ArchR#2296 · Filter by author dgodovich opened on Apr 9, 2025
  1

• How label Group list after integratin scRNA-seq and scATAC-seq data

  bug
  GreenleafLab/ArchR#2292 · Filter by author IqRaZaFaR16 opened on Apr 7, 2025
  3

• subsetArchRProject fails during barcode collisions between samples

  bug
  GreenleafLab/ArchR#2288 · Filter by author dgodovich opened on Apr 1, 2025
  2

• createArrowFiles has encountered an error

  bug
  GreenleafLab/ArchR#2287 · Filter by author Tc940417 opened on Mar 31, 2025
  1

• The fragment file exported by getGroupFragments() lacks reading support column

  bug
  GreenleafLab/ArchR#2283 · Filter by author Antidington opened on Mar 19, 2025
  2

• How to generate subplots?

  bug
  GreenleafLab/ArchR#2282 · Filter by author danli349 opened on Mar 17, 2025
  1

• Using ArchR for scATAc-seq

  bug
  GreenleafLab/ArchR#2280 · Filter by author IqRaZaFaR16 opened on Mar 7, 2025
  2

• Error in grid.Call.graphics(C_downvppath, name$path, name$name, strict): Viewport 'Norm. Enrichment -log10(P-adj) [0-Max]_heatmap_body_1_1' was not found

  bug
  GreenleafLab/ArchR#2279 · Filter by author IqRaZaFaR16 opened on Mar 7, 2025
  3

• Mismatch between gene expression and features

  bug
  GreenleafLab/ArchR#2277 · Filter by author TomVuod opened on Mar 3, 2025
  2

• Creating ARROWs

  bug
  GreenleafLab/ArchR#2276 · Filter by author karenpaiva opened on Feb 28, 2025
  1

• ArchR used for single sample .tsv file

  bug
  GreenleafLab/ArchR#2274 · Filter by author IqRaZaFaR16 opened on Feb 28, 2025
  1