README.md

In anthony-aylward/exploreatacseq: Exploratory Analysis of ATAC-seq data

exploreatacseq

Exploratory analysis of multiple ATAC-seq datasets

Installation

Standard

For a standard installation using a current version of R, do the following:

Install bioconductor if you haven't yet

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()

Then:

BiocManager::install(
  c(
    "BiocGenerics",
    "BiocParallel",
    "GenomicAlignments",
    "GenomicRanges",
    "IRanges",
    "Rsamtools",
    "S4Vectors",
    "SummarizedExperiment",
    "edgeR",
    "limma"
  )
)
install.packages(c("RColorBrewer", "jsonlite", "svglite", "uwot"))
library(devtools)
install_github("anthony-aylward/exploreatacseq")

Anaconda

If you are using Anaconda, you will need to install cairo and pkgconfig:

conda install -c anaconda cairo  
conda install -c anaconda pkgconfig

Older versions of R

If you are using an older version of R, you may need to switch to an older Bioconductor:

BiocManager::install(version="3.10")

Example usage

Here is an example JSON file that is formatted for use with exploreatacseq (see tssenrich for computation of TSS enrichment values). It includes three samples (SAMN10079665, SAMN09767462, AFA3256) and two treatment conditions (untreated, dexamethasone):

{
  "SAMN10079665": {
    "untreated": {
      "reads": "SAMN10079665_untreated.sort.filt.rmdup.bam",
      "tssenrich": 7.62,
      "peaks": "SAMN10079665_untreated_peaks.narrowPeak"
    },
    "dex": {
      "reads": "SAMN10079665_dex.sort.filt.rmdup.bam",
      "tssenrich": 6.67,
      "peaks": "SAMN10079665_dex_peaks.narrowPeak"
    }
  },
  "SAMN09767462": {
    "untreated": {
      "reads": "SAMN09767462_untreated.sort.filt.rmdup.bam",
      "tssenrich": 5.37,
      "peaks": "SAMN09767462_untreated_peaks.narrowPeak"
    },
    "dex": {
      "reads": "SAMN09767462_dex.sort.filt.rmdup.bam",
      "tssenrich": 5.16,
      "peaks": "SAMN09767462_dex_peaks.narrowPeak"
    }
  },
  "AFA3256": {
    "untreated": {
      "reads": "AFA3256_untreated.sort.filt.rmdup.bam",
      "tssenrich": 5.48,
      "peaks": "AFA3256_untreated_peaks.narrowPeak"
    },
    "dex": {
      "reads": "AFA3256_dex.sort.filt.rmdup.bam",
      "tssenrich": 5.88,
      "peaks": "AFA3256_dex_peaks.narrowPeak"
    }
  }
}

Assuming the above file is saved as atacseq.json, here is a simple example application of exploreatacseq in R:

library(exploreatacseq)

explore(
  "atacseq.json",
  "output_prefix",
  treatment_groups = list(c("untreated", "dex")),
  write_counts = TRUE,
  cores = 2
)

Example results

Here is an example of the visualization that can be achieved:

anthony-aylward/exploreatacseq documentation built on May 10, 2021, 8:45 a.m.