1 Introduction | 2 Methylation status calling on individual cytosines | 3 Methylation status calling on binned data | 4 Description of columns in the output | 5 Plots and enrichment analysis | 6 Export results | 7 Session Info
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:
methimpute_1.35.0.tar.gz
methimpute_1.35.0.zip(r-4.7)methimpute_1.35.0.zip(r-4.6)methimpute_1.35.0.zip(r-4.5)
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)
methimpute_1.35.0.tar.gz(r-4.7-arm64)methimpute_1.35.0.tar.gz(r-4.7-x86_64)methimpute_1.35.0.tar.gz(r-4.6-arm64)methimpute_1.35.0.tar.gz(r-4.6-x86_64)
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')) |
Datasets:
- arabidopsis_chromosomes - Chromosome lengths for Arabidopsis
- arabidopsis_genes - Gene coordinates for Arabidopsis
- arabidopsis_TEs - Transposable element coordinates for Arabidopsis
- arabidopsis_toydata - Toy data for Arabidopsis
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
Last updated from:a1c9caaca1. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 189 | ||
| linux-devel-arm64 | WARNING | 275 | ||
| linux-devel-x86_64 | WARNING | 306 | ||
| source / vignettes | OK | 300 | ||
| linux-release-arm64 | WARNING | 219 | ||
| linux-release-x86_64 | WARNING | 313 | ||
| macos-release-arm64 | WARNING | 136 | ||
| macos-release-x86_64 | WARNING | 515 | ||
| macos-oldrel-arm64 | WARNING | 169 | ||
| macos-oldrel-x86_64 | WARNING | 439 | ||
| windows-devel | WARNING | 239 | ||
| windows-release | WARNING | 252 | ||
| windows-oldrel | WARNING | 207 | ||
| wasm-release | OK | 175 |
Exports:binCountsbinMethylomebinomialTestMethylationbinPositionscallMethylationcallMethylationSeparatecollapseBinsdistanceCorrelationestimateTransDistexportMethylomeextractCytosinesFromFASTAgetDistinctColorsgetStateColorsimportBismarkimportBSMAPimportBSSeekerimportMethylpyinflateMethylomeloadFromFilesplotConvergenceplotEnrichmentplotHistogramplotPosteriorDistanceplotScatterplotTransitionProbs
Dependencies:askpassBiocGenericsBiostringsclicpp11crayoncurldata.tablefarvergenericsGenomeInfoDbGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglifecyclemagrittrmimeminpack.lmopensslplyrR6RColorBrewerRcppreshape2rlangS4VectorsS7scalesSeqinfostringistringrsysUCSC.utilsvctrsviridisLitewithrXVector
