Pipeline for Preparing Your Data
Learn how to format, normalize, and prepare your transcriptomic data for analysis. Accepted file types include counts, TPM, and FPKM.
About COMPASS Datasets
An overview of the datasets utilized in COMPASS.
SSL-based Pretraining on TCGA
Step-by-step guide for pretraining a Compass model from scratch.
The 2D UMAP Embedding of Pretrained Concepts and Genesets
Step-by-step guide for visualization of concepts.
Finetuning a New Model on an ICI Dataset
Step-by-step guide for offline model fine-tuning using COMPASS.
Making Predictions on a New Cohort
Instructions on running predictions and interpreting outputs.
Extract Features from COMPASS Model
How to extract useful features for developing new predictive models.
COMPASS Response Map (CRMap)
Personal CRMap for tracing the flow of information from gene expression through concept projection to final prediction.
COMPASS + Logistic Regression
Build a new LGR response prediction model based on COMPASS concepts.
COMPASS + CoxPH for Survival Prediction
Build a new CoxPH model based on COMPASS concepts.