Issues

• Monocle 3 order_cells won't select

  bug
  cole-trapnell-lab/monocle3#791 · Filter by author tesa1 opened on Sep 24, 2026
  1

• Clarification of "gene modules" in trajectory analysis

  cole-trapnell-lab/monocle3#789 · Filter by author sophia-heneghan opened on Aug 7, 2026

• How to solve pseudotime is Inf

  cole-trapnell-lab/monocle3#787 · Filter by author SSSJe opened on May 29, 2026
  2

• I don't know what to do

  bug
  cole-trapnell-lab/monocle3#785 · Filter by author jeff2240147683 opened on May 20, 2026
  1

• Fit_models apparently now rewuires package "reformulas

  bug
  cole-trapnell-lab/monocle3#784 · Filter by author KGSchilling opened on May 12, 2026
  3

• What's the internal normalization method for plot_genes_in_pseudotime?

  cole-trapnell-lab/monocle3#779 · Filter by author flybrain-lab opened on Apr 21, 2026

• plot_genes_hybrid should plot "zero" gene expression otherwise plots are not accurate

  cole-trapnell-lab/monocle3#777 · Filter by author eliza-barkan opened on Apr 6, 2026

• Error in tcrossprod(x, y): requires numeric/complex matrix/vector arguments

  bug
  cole-trapnell-lab/monocle3#769 · Filter by author boluofen opened on Dec 6, 2025
  1

• Plots render fine, but warnings about deprecated ggplot2 calls are printed

  cole-trapnell-lab/monocle3#767 · Filter by author oliviahelens opened on Oct 1, 2025
  1

• Use new_cell_data_set() to create a CDS object ,no error but rownames(CDS) =NULL

  cole-trapnell-lab/monocle3#766 · Filter by author Tsanhok opened on Aug 4, 2025
  1

• load_cellranger_data

  cole-trapnell-lab/monocle3#765 · Filter by author Lord-Kenny opened on Aug 1, 2025

• Multiomic trajectories (General Question)

  cole-trapnell-lab/monocle3#764 · Filter by author dsalinasduron-msmary opened on Jul 17, 2025

• tar of CDS object contains a full absolute path

  bug
  cole-trapnell-lab/monocle3#763 · Filter by author rfriedman22 opened on Jul 7, 2025

• Different trajectory graphing behavior after updating to R v4.5.1

  cole-trapnell-lab/monocle3#762 · Filter by author asitko opened on Jun 26, 2025
  1

• Regarding the clustering results of the UMAP graph generated independently using monocle3

  cole-trapnell-lab/monocle3#757 · Filter by author mosy550 opened on May 21, 2025

• Do you plan to upgrade monocle3 for Visium and spatial data?

  cole-trapnell-lab/monocle3#756 · Filter by author 532at opened on May 14, 2025

• matrixStats error with using align_cds

  cole-trapnell-lab/monocle3#751 · Filter by author marktopus opened on Mar 7, 2025
  4

• There seems to be no parameter in plot_cells to remove the border of the point

  bug
  cole-trapnell-lab/monocle3#750 · Filter by author huyulan-funan opened on Feb 26, 2025
  1

• Discrete time values after pseudotime

  cole-trapnell-lab/monocle3#748 · Filter by author roanvanscheppingen opened on Jan 20, 2025

• top_markers() error: 'list' object cannot be coerced to type 'double'

  cole-trapnell-lab/monocle3#747 · Filter by author soo-ni42 opened on Jan 20, 2025

• Monocle 3 using Seurat object and PHATE

  cole-trapnell-lab/monocle3#746 · Filter by author Yanst86 opened on Jan 16, 2025
  1

• Problems with root_cells

  cole-trapnell-lab/monocle3#745 · Filter by author Angle28 opened on Jan 16, 2025

• Problems with root_cells

  cole-trapnell-lab/monocle3#744 · Filter by author Angle28 opened on Jan 16, 2025

• Gene connectivity within each module

  bug
  cole-trapnell-lab/monocle3#741 · Filter by author sang-15 opened on Nov 25, 2024

• Interpretation of plots(repetitive numbers)

  cole-trapnell-lab/monocle3#740 · Filter by author jingsday opened on Nov 25, 2024