License: GPL-3
R build status


Authors: Brian Schilder, Jack Humphrey, Towfique Raj


README updated: Mar-15-2026

echoannot: Echoverse module: Functions for annotating genomic data

with annotations and epigenomic data.

This R package is part of the echoverse suite that supports echolocatoR: an automated genomic fine-mapping pipeline.

If you use echoannot, 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

Installation 

if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("RajLabMSSM/echoannot")
library(echoannot)

Documentation

Website

Getting started

Datasets

For more detailed information about each dataset, use ?:
R library(echolocatoR) ?NOTT_2019.interactome # example dataset

Epigenomic & genome-wide annotations

Nott et al. (2019)

  • Data from this publication contains results from cell type-specific (neurons, oligodendrocytes, astrocytes, microglia, & peripheral myeloid cells) epigenomic assays (H3K27ac, ATAC, H3K4me3) from human brain tissue.

  • For detailed metadata, see:

    data("NOTT_2019.bigwig_metadata")

  • Built-in datasets:

    • Enhancer/promoter coordinates (as GenomicRanges)
    data("NOTT_2019.interactome")
# Examples of the data nested in "NOTT_2019.interactome" object:
NOTT_2019.interactome$`Neuronal promoters`
NOTT_2019.interactome$`Neuronal enhancers`
NOTT_2019.interactome$`Microglia promoters`
NOTT_2019.interactome$`Microglia enhancers`
...
...
    • PLAC-seq enhancer-promoter interactome coordinates
    NOTT_2019.interactome$H3K4me3_around_TSS_annotated_pe
NOTT_2019.interactome$`Microglia interactome`
NOTT_2019.interactome$`Neuronal interactome`
NOTT_2019.interactome$`Oligo interactome`
...
...

  • API access to full bigWig files on UCSC Genome Browser, which includes

    • Epigenomic reads (as GenomicRanges)
    • Aggregate epigenomic score for each cell type - assay combination

Corces et al. (2020)

  • Data from this preprint contains results from bulk and single-cell chromatin accessibility epigenomic assays in 39 human brains.

    data("CORCES_2020.bulkATACseq_peaks")
data("CORCES_2020.cicero_coaccessibility")
data("CORCES_2020.HiChIP_FitHiChIP_loop_calls")
data("CORCES_2020.scATACseq_celltype_peaks")
data("CORCES_2020.scATACseq_peaks")

XGR

  • API access to a diverse library of cell type/line-specific epigenomic (e.g. ENCODE) and other genome-wide annotations.

Roadmap

  • API access to cell type-specific epigenomic data.

biomaRt

  • API access to various genome-wide SNP annotations (e.g. missense, nonsynonmous, intronic, enhancer).

HaploR

  • API access to known per-SNP QTL and epigenomic data hits.

Contact

Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience, Icahn School of Medicine at Mount Sinai