MOFA2
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bioFAM
Multi-Omics Factor Analysis
HI I am trying to create an mofa object and geeting the Seurat 5 error, which is already installed > Mofa1 packageVersion("Seurat") [1] ‘5.0.3’
I've found a single factor that I want to perform pathway enrichment on. When I try to run_enrichment but select only one factor, I get an error message. ``` pathways
I already set the GPU parameters to be true: train_opts$gpu_mode=TRUE ###################---------part of the log Model options: - Automatic Relevance Determination prior on the factors: True - Automatic Relevance Determination prior...
The prepare_mofa function runs without any error; howver, it didn't train the model. names(MOFAobject@expectations) returns NULL even after executing the prepare_mofa function. Can you please look into this and advise...
As of ggplot 3.3.4, I get this warning: ``` Warning: The `` argument of `guides()` cannot be `FALSE`. Use "none" instead as of ggplot2 3.3.4. ℹ The deprecated feature was...
Thank you for the great package, totally enjoy using it! Is there any mean to estimate uncertainty measures of the trained MOFA model? Like, e.g., in PCA one can estimate...
The `correlate_factors_with_covariates` function with `plot="r"` parameter has a title that does not fit into the plot boundaries. This is not something that a user can fix from the outside, because...
First of all, thank you for creating such an excellent R package. We've encountered several questions while using it: 1. Are there any potential issues with using genes obtained from...
For datasets that have a modality (and groups information) with N cells and another modality that has less than N cells, using the groups metadata for the second modality will...
Hey! I'm running MEFISTO on a 10X Visium sample based on the spatial transcriptomics tutorial. I have encountered an issue where some of the factors estimated by MEFISTO are all...
