Package: methylTFR 0.99.9

Irem B. Gündüz

methylTFR: Quantification of DNA Methylation Signatures in TFBS

methylTFR is an extensive R package designed specifically for analyzing DNA methylation signatures within transcription factor binding sites (TFBS) across diverse genomic annotations. It enhances methylation analysis by calculating a bias-corrected 'deviation' in methylation levels, leveraging GC bias distribution and frequency data. This package offers a variety of functions that facilitate the motif activity exhibiting diverse methylation patterns across distinct samples or cells.

Authors:Irem B. Gündüz [aut, cre], Sarath Kumar Murugan [aut], Fabian Mueller [aut], ERA-NET Transcan-Neu III - EPILUNAR [fnd], Saarland University [fnd]

methylTFR_0.99.9.tar.gz
methylTFR_0.99.9.zip(r-4.7-any)methylTFR_0.99.9.zip(r-4.6-any)methylTFR_0.99.9.zip(r-4.5-any)
methylTFR_0.99.9.tgz(r-4.6-any)methylTFR_0.99.9.tgz(r-4.5-any)
methylTFR_0.99.9.tar.gz(r-4.7-any)methylTFR_0.99.9.tar.gz(r-4.6-any)
methylTFR_0.99.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methylTFR/json (API)

# Install 'methylTFR' in R:
install.packages('methylTFR', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/epigenomeinformatics/methyltfr/issues

Pkgdown/docs site:https://epigenomeinformatics.github.io

On CRAN:

Conda:

softwarednamethylationsinglecellstatisticalmethodgeneregulationepigeneticstranscriptionsequencingwholegenomedifferentialmethylationmotifannotationmotifdiscoverycoverage

3.90 score 7 scripts 13 exports 58 dependencies

Last updated from:22b85e97f9. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE242
linux-develOK484
source / vignettesOK580
linux-releaseOK339
macos-releaseOK318
macos-oldrelOK337
windows-develOK371
windows-releaseOK462
windows-oldrelOK368
wasm-releaseOK261

Exports:addGCBintoMethylomecbindcomputeDeviationcomputeZScoreVariabilitydeviationsdeviationZScoresdifferential_deviation_testplotExpectedFootprintplotMotifFootprintrbindread_methylomerun_methyltfrrun_methylTFR_RnBeads

Dependencies:abindBHBiobaseBiocGenericsbiocmakeBiocParallelclicodetoolscpp11data.tableDelayedArraydir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableh5mreadHDF5ArrayIRangesisobandlabelinglambda.rlatticelifecycleloggermagrittrMatrixMatrixGenericsmatrixStatsR.methodsS3R.ooR.utilsR6RColorBrewerrhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentvctrsviridisLitewithrXVector

methylTFR: DNA Methylation Signatures in TFBS
Introduction | Installation | Getting Started | Read a Sample File | Annotation Resources | Input Data | Compute Deviation Score for a Single Sample and Single Motif | Run methylTFR on multiple samples and motifs | Run methylTFR directly on an RnBeads object | Session Information

Last update: 2026-09-29
Started: 2025-05-12

Case study: TF activity in memory vs. naive T cells
Introduction | The example dataset | Accessing the two assays | 1. Dimensionality reduction | 2. Differential TF activity | Ranking motifs by variability | Testing between two groups | Choosing an effect-size threshold | Visualising the differential motifs | 3. Comparing the two compartments | 4. Motif footprints | Observed and expected profiles | Bias-corrected footprint | References | Session Information

Last update: 2026-08-28
Started: 2026-07-22

Readme and manuals

Help Manual

Help pageTopics
addGCBintoMethylomeaddGCBintoMethylome
cbindcbind,methylTFRdeviations-method
computeDeviationcomputeDeviation
computeZScoreVariabilitycomputeZScoreVariability
deviationsdeviations
deviationsdeviations,methylTFRdeviations-method
deviationZScoresdeviationZScores
deviationZScoresdeviationZScores,methylTFRdeviations-method
differential_deviation_testdifferential_deviation_test
methylTFRdeviationsmethylTFRdeviations-class
plotExpectedFootprintplotExpectedFootprint
plotMotifFootprintplotMotifFootprint
rbindrbind,methylTFRdeviations-method
read_methylomeread_methylome
run_methyltfrrun_methyltfr
run_methylTFR_RnBeadsrun_methylTFR_RnBeads