Package: GIMP 0.2.0

GIMP: Genomic Imprinting Methylation Patterns

A package for analyzing Imprinting Control Regions (ICRs) DNA methylation. Supports both processed methylation data and raw IDAT files from Illumina arrays. Provides specialized tools for imprinting analysis including defect detection and interactive visualizations.

Authors:Abu Saadat [cre, aut], Francesco Cecere [aut]

GIMP_0.2.0.tar.gz
GIMP_0.2.0.zip(r-4.7-any)GIMP_0.2.0.zip(r-4.6-any)GIMP_0.2.0.zip(r-4.5-any)
GIMP_0.2.0.tgz(r-4.6-any)GIMP_0.2.0.tgz(r-4.5-any)
GIMP_0.2.0.tar.gz(r-4.7-any)GIMP_0.2.0.tar.gz(r-4.6-any)
GIMP_0.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GIMP/json (API)

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

Bug tracker:https://github.com/saadat-abu/gimp/issues

Datasets:

On CRAN:

Conda:

dnamethylationmicroarraypreprocessingqualitycontroldifferentialmethylationepigeneticsmethylationarraybioinformaticsmethylation-arraysshiny-app

2.60 score 2 stars 10 scripts 18 exports 192 dependencies

Last updated from:b3c382574a. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develWARNING1530
source / vignettesOK1261
linux-releaseWARNING1343
macos-releaseWARNING1751
macos-oldrelWARNING1433
windows-develWARNING1317
windows-releaseWARNING1160
windows-oldrelWARNING1331
wasm-releaseOK1233

Exports:calculate_detection_pvaluescheck_minfi_functionscreate_bedmethcreate_sample_sheet_templatediagnose_geo_datasetget_geo_phenotype_dataGIMP_appICRs_heatmapiDMPsmake_cpgsmake_ICRsplot_cpgs_coverageplot_line_ICRpreview_idat_zipprocess_geo_datasetprocess_geo_with_mappingsread_idat_zipvalidate_geo_dataset

Dependencies:abindannotateAnnotationDbiaskpassbackportsbase64base64encbeanplotBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocManagerBiocParallelBiostringsbitbit64bitopsblobbroombslibbumphuntercachemcellrangercigarilloclicliprcodetoolscommonmarkcpp11cpp11bigwigcrayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdir.expirydoParalleldoRNGdplyrDTevaluatefarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenefiltergenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2ggplotifygluegridGraphicsgtableh5mreadHDF5Arrayhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b4.hg19IlluminaHumanMethylationEPICmanifestIlluminaHumanMethylationEPICv2anno.20a1.hg38IlluminaHumanMethylationEPICv2manifestilluminaioIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslotelpheatmappillarpkgconfigplotlyplyrpngpreprocessCoreprettyunitsprogresspromisespurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrreadxlrematchrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsS7sassscalesscrimeselectrSeqinfoshinyshinydashboardsiggenessnowsourcetoolsSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextzdbutf8valrvctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlyulab.utils