Suzanne Jin

Update module: propr and propd to produce an optional output for GSEA/GREA

2

Optionally, when one wants to do GSEA or GREA aferwards, produce the output needed for it. So an adjacency matrix for GREA, and a gene list for GSEA.

### Is your feature request related to a problem? Please describe For current nf-core modules. We store a script inside the path `modules/nf-core/module_name/templates`. If one wants to run a process...

## PR checklist Closes #XXX - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be tested,...

Create a module that given a list of gene ids, it will fetch the GO concepts associated to each gene and the evidence code.

Question about differences between propr versions

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Hi @tpq ! While running propr using an older version (v4.0.0), I found that for some datasets different coefficients were obtained in comparison to the latest propr version. May I...

Question about scaling propr to very large data sets (Part 1)

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Hi Thom! Regarding the issue of large memory usage, I managed to reimplement what you proposed to me in the following pseudocode: ``` Alternatively, you could break down the whole...

Confusion about how the KEGG edges were filtered

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Hi! In the paper, you mentioned: > KEGG contains 290 pathways, and Reactome contains 1,581 pathways. For both, we only select directed edges with either activation or inhibition edge types...

Hello, I am training a regression model with ridge regression and self-defined samples. The same heldout data are used twice, so each model is outputting the predictions for each data...

Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data. source: https://github.com/KrishnaswamyLab/MAGIC ### Is there an existing module...

Deep count autoencoder for denoising scRNA-seq data source: https://github.com/theislab/dca ### Is there an existing module for this? - [X] I have searched for the existing module ### Is there an...