Package: methimpute 1.35.0

Aaron Taudt

methimpute: Imputation-guided re-construction of complete methylomes from WGBS data

This package implements functions for calling methylation for all cytosines in the genome.

Authors:Aaron Taudt

methimpute_1.35.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
methimpute/json (API)
NEWS

# Install 'methimpute' in R:
install.packages('methimpute', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On BioConductor:methimpute-1.35.0(bioc 3.24)methimpute-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologysoftwarednamethylationepigeneticshiddenmarkovmodelsequencingcoveragecppopenmp

4.18 score 15 scripts 436 downloads 1 mentions 25 exports 43 dependencies

Last updated from:a1c9caaca1. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
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linux-devel-arm64WARNING226
linux-devel-x86_64WARNING261
source / vignettesOK337
linux-release-arm64WARNING241
linux-release-x86_64WARNING272
macos-release-arm64WARNING143
macos-release-x86_64WARNING410
macos-oldrel-arm64WARNING198
macos-oldrel-x86_64WARNING336
windows-develWARNING235
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windows-oldrelWARNING194
wasm-releaseOK138

Exports:binCountsbinMethylomebinomialTestMethylationbinPositionscallMethylationcallMethylationSeparatecollapseBinsdistanceCorrelationestimateTransDistexportMethylomeextractCytosinesFromFASTAgetDistinctColorsgetStateColorsimportBismarkimportBSMAPimportBSSeekerimportMethylpyinflateMethylomeloadFromFilesplotConvergenceplotEnrichmentplotHistogramplotPosteriorDistanceplotScatterplotTransitionProbs

Dependencies:askpassBiocGenericsBiostringsclicpp11crayoncurldata.tablefarvergenericsGenomeInfoDbGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglifecyclemagrittrmimeminpack.lmopensslplyrR6RColorBrewerRcppreshape2rlangS4VectorsS7scalesSeqinfostringistringrsysUCSC.utilsvctrsviridisLitewithrXVector

Methylation status calling with METHimpute

Rendered frommethimpute.Rnwusingknitr::knitron May 26 2026.

Last update: 2018-06-12
Started: 2017-02-06

Readme and manuals

Help Manual

Help pageTopics
methIMPUTE: Imputation-guided methylation status calling for WGBS-seqmethimpute-package methimpute
Chromosome lengths for Arabidopsisarabidopsis_chromosomes
Gene coordinates for Arabidopsis (chr1)arabidopsis_genes
Transposable element coordinates for Arabidopsis (chr1)arabidopsis_TEs
Toy data for Arabidopsis (200.000bp of chr1)arabidopsis_toydata
Methimpute binning functionsbinCounts binMethylome binning binPositions
Call methylation statusbinomialTestMethylation
Call methylation statuscallMethylation
Call methylation statuscallMethylationSeparate
Collapse consecutive binscollapseBins
Distance correlationdistanceCorrelation
'transDist' parameterestimateTransDist
Export a methylomeexportMethylome
Extract cytosine coordinatesextractCytosinesFromFASTA
Get distinct colorsgetDistinctColors
Get original posteriorsgetPosteriors
Get state colorsgetStateColors
Methimpute data importimport importBismark importBSMAP importBSSeeker importMethylpy
Import a Rene methylation extractor fileimportRene
Inflate an imported methylation extractor fileinflateMethylome
Load 'methimpute' objects from fileloadFromFiles
methimpute objectsmethimpute-objects
methimputeBinomialHMMmethimputeBinomialHMM
methimputeDatamethimputeData
Perform a parameter scanparameterScan
Methimpute plotting functionsplotConvergence plotEnrichment plotHistogram plotPosteriorDistance plotScatter plotting plotTransitionProbs
Print model objectprint.methimputeBinomialHMM
Transform genomic coordinatestransCoord