MOFA2
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bioFAM
Multi-Omics Factor Analysis
Hi, I have peak datasets for different sequencing types, eg. atac, histone modifications, etc across multiple samples. I want to cluster peaks (features) along with samples. can I use MOFA+...
Hello everyone, First, I just wanted to express my thanks for the software; especially tutorials, documentation, and explanations. Those are some of the main reasons I enjoy using the MOFA...
My R just crashes when I run the last step using run_mofa, I have tried reducing the number of features, and also reinstalled basilisk. Could you help me take a...
Hi, I'd like to use the `spikeslab_factors` option, but it is broken on the mofapy2 version installed by basilisk. The issue was fixed on mofapy2 0.7.1: https://github.com/bioFAM/mofapy2/issues/17 The latest release...
Hello, I would like to try MOFA+ for some CITE-Seq data and I was wondering if you could provide some recommendations on how to deal with batch effects. We‘re generally...
I’m using MOFA2 on bulk multi-omics data (methylation and gene expression) with ~95k CpG sites and ~20k genes across 270 samples. While creating the MOFA object, I get the error:...
My colleague was analyzing her data and received the following warning: ``` Warning message: In .quality_control(object, verbose = verbose) : Factor(s) 1 are strongly correlated with the total number of...
Dear all, I run python 3.11 mu.tl.mofa(mdata, use_obs='union', convergence_mode='medium', outfile=f'Saved_models/mofatalk{combo}.h5ad', n_factors=4, ) model = mofa.mofa_model(f"Saved_models/mofatalk{combo}.h5ad") lead to 'ascii' codec can't decode byte 0xce in position 2: ordinal not in range(128)...
Dear developers, has anybody every quantified the difference between how long it takes to train the mofa model on cpu or gpu? I tried running your sample scripts and to...
