methylTFR : Quantification of DNA Methylation Patterns in TFBS

methylTFR is an R-package to analyze DNA methylation signatures in transcription factor binding sites in each individual cells or samples.

Installation instructions

Get the latest release methylTFR from Bioconductor using the following code:

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

BiocManager::install("methylTFR")

And the development version from GitHub with:

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("EpigenomeInformatics/methylTFR")

Documentation

Full documentation and vignettes are hosted at epigenomeinformatics.github.io/methylTFR:

• Get started — reading data, computing deviations, and footprints.
• Case study: memory vs. naive T cells — differential TF activity on bundled example data.

Quick Start

This is a basic example which shows you how to run methylTFR :

library(GenomicRanges)
library(dplyr)
library(methylTFRAnnotationHg38) # annotation package for hg38
library(methylTFR)

gcfreqs <- getGCfreq(motifSet = "jaspar2020")
gc_dist <- getGenomeGC()
tf_bindsites <- getTFbindsites(motifSet = "jaspar2020")

sample_dir <- file.path("samples_dir")
sample_ann <- "samples.tsv" # should contain column name bedFile

# deviation score matrix
deviations <- run_methyltfr(sample_ann, # sample annotation file
  sample_dir, # where the EPP files are
  threads = 8, # number of threads
  chunkSize = 10, # number of chunks to process
  sampleColName = "bedFile", # column name for EPP file paths in sample_ann
  tf_bindsites = tf_bindsites, # TF binding sites
  gcfreqs = gcfreqs, # GC frequency
  gc_dist = gc_dist, # GC distribution
  filetype = "EPP" # file type
)

Citation

If you use methylTFR in your work, please cite:

Gunduz IB, Murugan SK, Mueller F (2026). methylTFR: Quantification of DNA methylation signatures in TFBS. R package version 0.99.9. https://github.com/EpigenomeInformatics/methylTFR

@Manual{methylTFR,
  title = {methylTFR: Quantification of DNA methylation signatures in TFBS},
  author = {Irem B. Gunduz and Sarath Kumar Murugan and Fabian Mueller},
  year = {2026},
  note = {R package version 0.99.9},
  url = {https://github.com/EpigenomeInformatics/methylTFR},
  doi = {10.18129/B9.bioc.methylTFR},
}

Run citation("methylTFR") in R to get the entry for the version you have installed.