monocle3

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Install leidenbase and monocle3 on M1 mac

3

Hi, I'm trying to install monocle3 on an M1 mac. I can't seem to get passed the dependency leidenbase. Has anyone successfully installed both on an M1 Mac, if so,...

RodrigoGM

Error installing monocle3 in windows

1

Hi, I am facing issues in installing monocle3 on Windows. I have installed the dependencies, and the error shows. **sh: -c: line 1: unexpected EOF while looking for matching `''...

VilainLab

I am following the vignette for projecting a query data set onto a reference data set https://cole-trapnell-lab.github.io/monocle3/docs/projection/ as I have done successfully previously. However, with my current data sets I...

mreg05

Problem downloading Monocle3 dependencies (terra) on M1 Pro MacBook

4

**Describe the bug** - I am unable to download the Monocle3 dependencies ('terra') from Biocmanager **To Reproduce** > library(BiocManager) Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) > BiocManager::install(c('BiocGenerics', 'DelayedArray',...

garrett-lam

cds

CJSCI666

Hello, I found the below response from a 2 year-old issue. Are there any updates or workarounds for the interactive parts of the monocle for the server? It would be...

erkinacar5

Error while trying to install monocle3

3

I’m running into errors while trying to install monocle3 onto my R studio using R version 4.2.1 on my macbook pro 2022 (M2 chip): Here are the commands that I...

techgirl2022

Hi I am trying to fully understand the Monocle 3 algorithm. If I cannot find enough description of some steps in your documentation/publications I check it in the source code....

marlena-D4C

cell_stroke removal

1

Hi, I recently re-downlaoded monocle3 and now in every plot_cells UMAP the cells of each cluster are shadowed by cell_stroke. I've tried to bring it down as much as possible...

legeinei123

Monocle 3 error: plot_cells(cds, color_cells_by="cao_cell_type") gives the following error:color_cells_by must one of 'cluster', 'partition', 'pseudotime, or a column in the colData table.

4

How do I correct the above error? I have loaded the my scRNA data using load_mm_data. Please help. And before that step, I received the following: plot_cells(cds) No trajectory to...

yojetsharma