Package 'fluentGenomics'

Title: A plyranges and tximeta workflow
Description: An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.
Authors: Stuart Lee [aut, cre] (ORCID: <https://orcid.org/0000-0003-1179-8436>), Michael Love [aut, ctb]
Maintainer: Stuart Lee <[email protected]>
License: MIT + file LICENSE
Version: 1.24.0
Built: 2026-10-04 17:15:25 UTC
Source: https://github.com/bioc/fluentGenomics

Help Index

Download, retrieve and cache macrophage ATAC seq results

Description

Download, retrieve and cache macrophage ATAC seq results

Usage

cache_atac_se(verbose = FALSE)

Arguments

verbose

Provide progress bar for downloading and updating the cache? (Default is FALSE)

Details

This code generates the SummarizedExperiment object used for ATAC seq peaks data analysis as discussed in the vignette.

Value

the path to the .rds file containing the SummarizedExperiment

Source

https://zenodo.org/record/1188300/files/

Examples

if (interactive()) {
 path_to_se <- cache_atac_se()
 atac <- readRDS(path_to_se)
}

Summarised ATAC-seq peaks as a GRanges object

Description

A GRanges object containing approximately 300,000 differential accessiblity peaks estimated via limma. A description of how this object was generated can be found in the vignette.

Usage

peaks

Format

An object of class GRanges of length 296220.

Details

#' @format A GRanges with 296220 rows and 3 metadata columns:

peak_id

the ATAC peak identifer

da_log2FC

the estimated log2 fold change

da_padj

the estimated differential accessibility FDR adjusted p-value