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
methimpute_1.35.0.zip(r-4.7-x86_64)methimpute_1.35.0.zip(r-4.7-arm64)methimpute_1.35.0.zip(r-4.6-x86_64)methimpute_1.35.0.zip(r-4.6-arm64)methimpute_1.35.0.zip(r-4.5-x86_64)
methimpute_1.35.0.tgz(r-4.6-x86_64)methimpute_1.35.0.tgz(r-4.6-arm64)methimpute_1.35.0.tgz(r-4.5-x86_64)methimpute_1.35.0.tgz(r-4.5-arm64)
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methimpute_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
methimpute/json (API)

# 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

3.28 score 19 scripts 608 downloads 1 mentions 25 exports 43 dependencies

Last updated from:a1c9caaca1. Checks:2 ERROR, 13 WARNING, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR223
linux-devel-arm64WARNING201
linux-devel-x86_64WARNING325
source / vignettesERROR3241
linux-release-arm64WARNING180
linux-release-x86_64WARNING272
macos-release-arm64WARNING187
macos-release-x86_64WARNING325
macos-oldrel-arm64WARNING216
macos-oldrel-x86_64WARNING450
windows-devel-arm64WARNING330
windows-devel-x86_64WARNING313
windows-release-arm64WARNING327
windows-release-x86_64WARNING198
windows-oldrel-x86_64WARNING211
wasm-releaseOK124

Exports:binCountsbinMethylomebinomialTestMethylationbinPositionscallMethylationcallMethylationSeparatecollapseBinsdistanceCorrelationestimateTransDistexportMethylomeextractCytosinesFromFASTAgetDistinctColorsgetStateColorsimportBismarkimportBSMAPimportBSSeekerimportMethylpyinflateMethylomeloadFromFilesplotConvergenceplotEnrichmentplotHistogramplotPosteriorDistanceplotScatterplotTransitionProbs

Dependencies:askpassBiocGenericsBiostringsclicpp11crayoncurldata.tablefarvergenericsGenomeInfoDbGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglifecyclemagrittrmimeminpack.lmopensslplyrR6RColorBrewerRcppreshape2rlangS4VectorsS7scalesSeqinfostringistringrsysUCSC.utilsvctrsviridisLitewithrXVector

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