README.md

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

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.

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Contact

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