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License: GPL-3
R build status

Authors: Brian Schilder, Jack Humphrey, Towfique Raj

README updated: Oct-20-2023

echoannot: 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:

Installation

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

remotes::install_github("RajLabMSSM/echoannot")
library(echoannot)

Documentation

Datasets

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

Epigenomic & genome-wide annotations

  • 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
  • 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")
  • API access to a diverse library of cell type/line-specific epigenomic (e.g. ENCODE) and other genome-wide annotations.
  • API access to cell type-specific epigenomic data.
  • API access to various genome-wide SNP annotations (e.g. missense, nonsynonmous, intronic, enhancer).
  • 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