echoAI: API access to variant-level AI/ML predictions including IMPACT (Inference and Modeling of Phenotype-related ACtive Transcription) for immune cell annotations. Part of the echoverse suite for genomic fine-mapping.
This R package is part of the echoverse suite that supports
echolocatoR: an automated
genomic fine-mapping pipeline.
If you use echoAI, please cite:
Brian M. Schilder, Jack Humphrey, Towfique Raj (2021) echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline, Bioinformatics; btab658, https://doi.org/10.1093/bioinformatics/btab658
if(!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("RajLabMSSM/echoAI")
library(echoAI)IMPACT_query(): Query IMPACT annotations and LD-scores from tabix-indexed files on Zenodo. Supports wide, long, and list output formats.IMPACT_get_annotations(): Download raw IMPACT annotation matrices from GitHub and merge with your variant data.IMPACT_get_annotation_key(): Retrieve the IMPACT annotation key describing tissue, cell type, and transcription factor metadata for all 707 annotations.
IMPACT_compute_enrichment(): Compute enrichment of IMPACT scores across SNP groups (lead GWAS, credible sets, consensus).IMPACT_iterate_enrichment(): Run enrichment tests across all loci.
IMPACT_snp_group_boxplot(): Box/violin plot of IMPACT scores by SNP group with statistical comparisons.IMPACT_plot_enrichment(): Bar and violin plots summarising enrichment results.IMPACT_plot_impact_score(): Multi-panel locus plot combining GWAS, fine-mapping, and per-tissue IMPACT scores.IMPACT_heatmap(): ComplexHeatmap of mean IMPACT scores across loci and SNP groups.
Brian M. Schilder, Bioinformatician II Raj Lab Department of Neuroscience, Icahn School of Medicine at Mount Sinai