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Error with downstream tasks from genome = BSgenome.Mmusculus.UCSC.mm10

Status: Open.

#33 In CostaLab/scMEGA;

· alifarhat40 opened on Mar 14, 2026

The CreatePairedObject function contains a logic error that leads to mismatched counts matrices between ATAC and RNA modalities.

Status: Open.

#32 In CostaLab/scMEGA;

· noralis-bit opened on Jun 20, 2025

Error in irlba(A = t(x = object), nv = n, work = irlba.work, tol = tol) : function 'as_cholmod_sparse' not provided by package 'Matrix'

Status: Open.

#31 In CostaLab/scMEGA;

· zly19980908 opened on Mar 27, 2025

Gene-regulatory network of pbmc

Status: Open.

#30 In CostaLab/scMEGA;

· watermelon-flower opened on Nov 19, 2024

Why CreatePairedObject is not working?

Status: Open.

#29 In CostaLab/scMEGA;

· venkan opened on Apr 25, 2024

CoembedData - Error: None of the provided refdata elements are valid.

Status: Open.

#27 In CostaLab/scMEGA;

· kylepalos opened on Oct 22, 2023

error in SelectTFs or GetTrajectory

Status: Open.

#25 In CostaLab/scMEGA;

· rahulnutron opened on Sep 11, 2023

Incompability with Seurat v5

Status: Open.

#24 In CostaLab/scMEGA;

· lzj1769 opened on Jul 28, 2023

problem with SelectTFs

Status: Open.

#23 In CostaLab/scMEGA;

· Dalhte opened on Jul 26, 2023

NetCentPlot error

Status: Open.

#21 In CostaLab/scMEGA;

· liyang24 opened on May 17, 2023

Motif matching when using mouse data

enhancementNew feature or requestNew feature or request

Status: Open.

#18 In CostaLab/scMEGA;

· AmandaKedaigle opened on Mar 15, 2023

SelectGenes use other genome

Status: Open.

#17 In CostaLab/scMEGA;

· liyang24 opened on Mar 13, 2023