README.md

In RajLabMSSM/echoannot: echoverse module: Annotate fine-mapping results

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:

r data("NOTT_2019.bigwig_metadata")

• Built-in datasets:

• Enhancer/promoter coordinates (as GenomicRanges)

r 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

r 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.

r 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

RajLabMSSM/echoannot documentation built on Oct. 26, 2023, 2:41 p.m.