Use Cases

This section contains use cases demonstrating how to use Coala in various scenarios.

Gene Variant Analysis

This use case demonstrates how to use Coala to perform query-dirven gene-variant analysis: retrieving gene coordinates from NCBI, extracting variants from ClinVar VCF files, filtering by clinical significance, and performing detailed variant annotation.

RNA-Seq Analysis

This use case demonstrates how to use Coala to perform query-driven RNA-Seq analysis: downloading data from GEO, describing study design information, performing differential gene expression (DEG) analysis, downloading curated gene sets from MSigDB, running Gene Set Enrichment Analysis (GSEA) with canonical pathways, and generating enrichment plots for specified pathways.

ATAC-Seq Analysis

This use case demonstrates how to use Coala to perform query-driven ATAC-Seq analysis, including peak calling using MACS3, peak annotation using ChIPseeker, and peak visualization using pyGenomeTracks.

Hi-C Analysis

This use case demonstrates how to use Coala to perform query-driven Hi-C analysis and visualization. We use cooler and cooltools to visualize chromatin contact maps, compartmentalize chromosome into active (A) and inactive (B) regions, and indentify boundaries between topologically associating domains (TADs).