Package: methimpute 1.29.0

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

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methimpute.pdf |methimpute.html✨
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NEWS

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On BioConductor:methimpute-1.29.0(bioc 3.21)methimpute-1.28.0(bioc 3.20)

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

immunooncologysoftwarednamethylationepigeneticshiddenmarkovmodelsequencingcoveragecppopenmp

4.11 score 13 scripts 212 downloads 1 mentions 25 exports 54 dependencies

Last updated 2 months agofrom:4287169a23. Checks:OK: 1 WARNING: 7 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64WARNINGNov 29 2024
R-4.5-linux-x86_64WARNINGNov 29 2024
R-4.4-win-x86_64WARNINGNov 29 2024
R-4.4-mac-x86_64WARNINGNov 29 2024
R-4.4-mac-aarch64WARNINGNov 29 2024
R-4.3-win-x86_64NOTENov 29 2024
R-4.3-mac-x86_64WARNINGNov 29 2024
R-4.3-mac-aarch64WARNINGNov 29 2024

Exports:binCountsbinMethylomebinomialTestMethylationbinPositionscallMethylationcallMethylationSeparatecollapseBinsdistanceCorrelationestimateTransDistexportMethylomeextractCytosinesFromFASTAgetDistinctColorsgetStateColorsimportBismarkimportBSMAPimportBSSeekerimportMethylpyinflateMethylomeloadFromFilesplotConvergenceplotEnrichmentplotHistogramplotPosteriorDistanceplotScatterplotTransitionProbs

Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurldata.tablefansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimeminpack.lmmunsellnlmeopensslpillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangS4VectorsscalesstringistringrsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Methylation status calling with METHimpute

Rendered frommethimpute.Rnwusingknitr::knitron Nov 29 2024.

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