Kristoffer Vitting-Seerup

Inclusion of variable not to regress out

2

Thanks for a very interesting paper and very useful tool. Is there a way to include factors not to regress out (e.g. like ```limma::removeBatchEffect()```? An example could be I have...

small suggestions

5

I've been using ```run.Ted``` a few times now and I've made a couple observations which results in TED giving uninformative error message. These should be easy for you to implement...

BAM files where sequences have been removed (due to privacy issues) are quite commen - can Bazam use a refrence genome to extract the corresponding sequences?

[Independent Enrichment Analysis] Bug in background?

2

I've recently started using your [Appyter for Independent Enrichment Analysis](https://appyters.maayanlab.cloud/Independent_Enrichment_Analysis/) to analyze the Enrichr catalog with a costume background. But because I kept getting very large odds ratios and very...

In the [caret book](https://topepo.github.io/caret/train-models-by-tag.html#handle-missing-predictor-data) would it not be correct to add the "gbm" method (gbm::gbm) to the "handling missing predictor data" section? Cheers Kristoffer

Is singscore usable on single cell data?

5

Is singscore usable on single cell data? If so are there specific parameters you recommend?