transcriptionfactory/jishnulabtools

JishnuLabTools

See the (properly formatted) HTML vignette

https://htmlpreview.github.io/?https://github.com/TranscriptionFactory/JishnuLabTools/blob/main/running_ER_on_cluster.html

vignette for SLIDE

https://htmlpreview.github.io/?https://github.com/TranscriptionFactory/JishnuLabTools/blob/main/running_slide.html

Mostly tools for running Essential Regression (ER) and Significant Latent Factor Interaction Discovery and Exploration (SLIDE)

Read the publications:

1. Essential Regression

• https://www.cell.com/patterns/pdfExtended/S2666-3899(22)00053-8
• Github: See SLIDEpre repo below

2. SLIDE

• (preprint) https://www.biorxiv.org/content/10.1101/2022.11.25.518001v1.full.pdf
• Github: https://github.com/jishnu-lab/SLIDE

Heuristics for running ER

1. There are two important tuning variables: delta and lambda
2. Delta is more important and controls the number of latent factors
3. Lambda is less important and controls how latent factors are related

There are example yamls provided for regression and classification:

JishnuLabTools::regression_params
JishnuLabTools::classification_params