Artur Sannikov

`correlate_covariates`: redundant conversion to numeric and incorrect warning

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In `correlate_covariates.R` on [line 52](https://github.com/bioFAM/MOFA2/blob/master/R/correlate_covariates.R#L52) the code converts the columns to numeric twice with a warning in between. Line 56 is not required. We can throw a warning and then...

`get_factors` and `get_variance_explained` have the same description in documentation: > Extract the latent factors from the model. However, `get_variance_explained` does not extract latent factors but variance per view per factor.

`?plot_top_weights` In Details it says: > This function displays the top features with highest loading whereas the function [plot_top_weights](http://127.0.0.1:32209/help/library/MOFA2/help/plot_top_weights) plots all weights for a given latent factor and view. I...

Links on [Documentation page](https://biofam.github.io/MOFA2/documentation.html) are: * Outdated for MOFA2 R package. The correct link is on [Bioconductor](https://bioconductor.org/packages/release/bioc/html/MOFA2.html): https://bioconductor.org/packages/release/bioc/manuals/MOFA2/man/MOFA2.pdf * Incorrect for Python packages. It's the same outdated link for R...

Hello, it's not an issue with the package. In [README](https://github.com/mixOmicsTeam/mixOmics/blob/master/README.md) file, the link (https://mixomicsteam.github.io/Bookdown/) in section "Want to know more?" leads to 404. The correct link is https://mixomicsteam.github.io/mixOmics-Vignette/

Docs: how to run Stirling PDF with Podman Quadlet

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It's possible to run Stirling PDF as a Podman [Quadlet](https://www.redhat.com/sysadmin/quadlet-podman) with Podman 4.4+. Here is the Quadlet I use to run it locally: ``` [Container] Image=docker.io/frooodle/s-pdf:latest AutoUpdate=registry PublishPort=8080:8080 Volume=/location/of/trainingData:/usr/share/tesseract-ocr/5/tessdata Volume=/location/of/logs/logs:/logs...

I said that I'm using Podman quadlet in #1068. For this issue, I used this .container file ``` [Container] Image=docker.io/frooodle/s-pdf:latest AutoUpdate=registry PublishPort=8080:8080 Volume=/location/of/trainingData:/usr/share/tesseract-ocr/5/tessdata:Z Volume=/location/of/logs/logs:/logs:Z [Service] Restart=always [Install] WantedBy=default.target ```` The...

Since this version will not be updated, maybe you can archive it?

Similarly to #148, [links](https://biofam.github.io/MOFA2/tutorials.html) to tutorials are outdated. * [Training a MOFA model in R](https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/getting_started_R.html) should link to [here](https://bioconductor.org/packages/release/bioc/vignettes/MOFA2/inst/doc/getting_started_R.html). * [Downstream analysis in R](https://raw.githack.com/bioFAM/MOFA2_tutorials/master/R_tutorials/downstream_analysis.html) shoud link to [here](https://bioconductor.org/packages/release/bioc/vignettes/MOFA2/inst/doc/downstream_analysis.html).

Warning:The assays in your SummarizedExperiment have row names, but they don't agree with the row names of the SummarizedExperiment object itself

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Reposting from Slack. When creating a new column in a `tse` object, I get `Warning: tidySummarizedExperiment says: the assays in your SummarizedExperiment have row names, but they don't agree with...