Package: methylTFR 0.99.9
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:
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
softwarednamethylationsinglecellstatisticalmethodgeneregulationepigeneticstranscriptionsequencingwholegenomedifferentialmethylationmotifannotationmotifdiscoverycoverage
Last updated from:22b85e97f9. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 242 | ||
| linux-devel | OK | 484 | ||
| source / vignettes | OK | 580 | ||
| linux-release | OK | 339 | ||
| macos-release | OK | 318 | ||
| macos-oldrel | OK | 337 | ||
| windows-devel | OK | 371 | ||
| windows-release | OK | 462 | ||
| windows-oldrel | OK | 368 | ||
| wasm-release | OK | 261 |
Exports:addGCBintoMethylomecbindcomputeDeviationcomputeZScoreVariabilitydeviationsdeviationZScoresdifferential_deviation_testplotExpectedFootprintplotMotifFootprintrbindread_methylomerun_methyltfrrun_methylTFR_RnBeads
Dependencies:abindBHBiobaseBiocGenericsbiocmakeBiocParallelclicodetoolscpp11data.tableDelayedArraydir.expiryfarverfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableh5mreadHDF5ArrayIRangesisobandlabelinglambda.rlatticelifecycleloggermagrittrMatrixMatrixGenericsmatrixStatsR.methodsS3R.ooR.utilsR6RColorBrewerrhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentvctrsviridisLitewithrXVector
Last update: 2026-09-29
Started: 2025-05-12
Last update: 2026-08-28
Started: 2026-07-22
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| addGCBintoMethylome | addGCBintoMethylome |
| cbind | cbind,methylTFRdeviations-method |
| computeDeviation | computeDeviation |
| computeZScoreVariability | computeZScoreVariability |
| deviations | deviations |
| deviations | deviations,methylTFRdeviations-method |
| deviationZScores | deviationZScores |
| deviationZScores | deviationZScores,methylTFRdeviations-method |
| differential_deviation_test | differential_deviation_test |
| methylTFRdeviations | methylTFRdeviations-class |
| plotExpectedFootprint | plotExpectedFootprint |
| plotMotifFootprint | plotMotifFootprint |
| rbind | rbind,methylTFRdeviations-method |
| read_methylome | read_methylome |
| run_methyltfr | run_methyltfr |
| run_methylTFR_RnBeads | run_methylTFR_RnBeads |
