MOFA2

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AttributeError: Module 'scipy' has no attribute 'random'

5

I am running into an issue when trying to follow the tutorial provided by the creator. It states that "AttributeError: Module 'scipy' has no attribute 'random'". This are my python...

ahucke

Dear developers, > Importantly, the weights of the features within a view have relative values and they should not be interpreted in an absolute scale. Therefore, for interpretability purposes we...

gmhhope

Way to save model directly in R

1

Hi there, thanks for providing such a package. When I preform MOFA, I sometimes need to update the sample metadata after running the model. Is there a way I could...

hsiaoyi0504

Strategies using MOFA for integrating proteomic and CyTOF data

1

Hello, I had a general question about using MOFA. I recently tried using MOFA to explore some proteomic (359 features) and CyTOF (37 features) in a cohort of 89 patient...

pdimitron

Hello: I saw the tutorial for Single Cell Multiome analysis (https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/10x_scRNA_scATAC.html), could I analyze bulk RNAseq and bulk ATACseq together using `MOFA2`? Is there a tutorial for this kind of...

danli349

> MOFAobject.trained Available versions Package __glibc conflicts for: @/linux-64::__glibc==2.35=0 python=3.7.7 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17'] Note that strict channel priority may have removed packages required for satisfiability. Error: Error creating conda...

HeenaBioinfo

Error in py_call_impl(callable, dots$args, dots$keywords): AttributeError: Module 'scipy' has no attribute 'random'

8

I have installed a conda env with mofapy. ``` > reticulate::py_config() python: /home/roy/miniconda3/envs/mofa/bin/python libpython: /home/roy/miniconda3/envs/mofa/lib/libpython3.10.so pythonhome: /home/roy/miniconda3/envs/mofa:/home/roy/miniconda3/envs/mofa version: 3.10.6 (main, Oct 24 2022, 16:07:47) [GCC 11.2.0] numpy: /home/roy/miniconda3/envs/mofa/lib/python3.10/site-packages/numpy numpy_version: 1.23.4...

royfrancis

When R_HOME path contains space like "/Program Files/", Rcmd returns a failed message ``` -- R CMD build ---------------------------------------------------------------------------------------------------- v checking for file 'C:\Users\***\AppData\Local\Temp\RtmpOovcjo\remotes47205def466f\bioFAM-MOFA2-6ccdc73/DESCR' - preparing 'MOFA2': v checking DESCRIPTION...

liuhuoz

Hi there, I have a question/suggestion about the MOFA2::calculate_contribution_scores function which "calculates, *for each sample* how much each view contributes to its location in the latent manifold". This was exactly...

ChristianRohde

model_opts$spikeslab_weights <- TRUE

3

Hi there, it took me a while to understand why my MOFA2 analyses with version 1.4.0 are so different from 1.8.0. With the latest version I had to manually add...

ChristianRohde