Package: methInheritSim 1.29.0

Pascal Belleau

methInheritSim: Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.

Authors:Pascal Belleau, Astrid Deschênes and Arnaud Droit

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methInheritSim.pdf |methInheritSim.html✨
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NEWS

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

Peer review:

Bug tracker:https://github.com/belleau/methinheritsim/issues

Datasets:
  • dataSimExample - A 'list' containing methylation information used by some internal functions (for demo purpose.
  • samplesForChrSynthetic - All samples information, formated by 'methylKit', in a 'methylBase' format (for demo purpose).

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

biologicalquestionepigeneticsdnamethylationdifferentialmethylationmethylseqsoftwareimmunooncologystatisticalmethodwholegenomesequencingbisulphite-sequencinginheritancemethylationsimulation

4.60 score 1 stars 1 scripts 236 downloads 1 exports 101 dependencies

Last updated 2 months agofrom:7089998862. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winNOTEDec 19 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winNOTEDec 19 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winNOTEDec 19 2024
R-4.3-macNOTEDec 19 2024

Exports:runSim

Dependencies:abindaskpassbbmlebdsmatrixBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodacodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayemdbookexpmfansifarverfastsegformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmethylKitmgcvmimemsmmunsellmvtnormnlmenumDerivopensslpillarpkgconfigplyrqvalueR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreshape2restfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc

Simulating Whole-Genome Inherited Bisulphite Sequencing Data

Pascal Belleau, Astrid Deschênes and Arnaud Droit

Rendered frommethInheritSim.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-09-29
Started: 2017-03-30