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:

bed450k - BED 450K probes
bedEPICv1 - BED EPICv1 probes
bedEPICv2 - BED EPICv2 probes
DMRs.hg19 - Imprinted Regions
DMRs.hg38 - Imprinted Regions

On CRAN:

dnamethylation microarray preprocessing qualitycontrol differentialmethylation epigenetics methylationarray bioinformatics methylation-arrays shiny-app

2.65 score 1 stars 10 scripts 18 exports 192 dependencies

Last updated from:1c3e55f695. Checks:7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	1434
source / vignettes	OK	1265
linux-release-x86_64	WARNING	1497
macos-release-arm64	WARNING	1076
macos-oldrel-arm64	WARNING	1193
windows-devel	WARNING	1073
windows-release	WARNING	1377
windows-oldrel	WARNING	1283
wasm-release	OK	1373

Exports:calculate_detection_pvalues check_minfi_functions create_bedmeth create_sample_sheet_template diagnose_geo_dataset get_geo_phenotype_data GIMP_app ICRs_heatmap iDMPs make_cpgs make_ICRs plot_cpgs_coverage plot_line_ICR preview_idat_zip process_geo_dataset process_geo_with_mappings read_idat_zip validate_geo_dataset

Dependencies:abind annotate AnnotationDbi askpass backports base64 base64enc beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob broom bslib bumphunter cachem cellranger cigarillo cli clipr codetools commonmark cpp11 cpp11bigwig crayon crosstalk curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doParallel doRNG dplyr DT evaluate farver fastmap filelock fontawesome foreach formatR fs futile.logger futile.options genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 ggplotify glue gridGraphics gtable h5mread HDF5Array highr hms htmltools htmlwidgets httpuv httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICv2anno.20a1.hg38 IlluminaHumanMethylationEPICv2manifest illuminaio IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl otel pheatmap pillar pkgconfig plotly plyr png preprocessCore prettyunits progress promises purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr readxl rematch rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 sass scales scrime selectr Seqinfo shiny shinydashboard siggenes snow sourcetools SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex tzdb utf8 valr vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml yulab.utils

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BED 450K probes	bed450k
BED EPICv1 probes	bedEPICv1
BED EPICv2 probes	bedEPICv2
Alternative Detection P-value Calculation	calculate_detection_pvalues
Check Available minfi Functions	check_minfi_functions
Create BED File Data from Methylation Array Annotations	create_bedmeth
Create Sample Sheet Template	create_sample_sheet_template
Diagnose GEO dataset structure	diagnose_geo_dataset
Imprinted Regions	DMRs.hg19
Imprinted Regions	DMRs.hg38
Get phenotypic data preview for GEO dataset	get_geo_phenotype_data
Launch GIMP Shiny Application	GIMP_app
Generate Heatmap of ICRs Methylation	ICRs_heatmap
Identify Differentially Methylated Positions in ICRs	iDMPs
Create ICR CpG Matrix	make_cpgs
Create the ICR Matrix	make_ICRs
Plot ICR CpG Matrix with Counts and Percentage Coverage	plot_cpgs_coverage
Plot Line Plot for ICR Methylation	plot_line_ICR
Preview IDAT ZIP Contents	preview_idat_zip
Download and process GEO methylation dataset	process_geo_dataset
Process GEO dataset with user-specified group mappings	process_geo_with_mappings
Read IDAT Files from ZIP Archive This function extracts and processes IDAT files from a ZIP archive containing IDAT files and a sample sheet, returning a beta value matrix ready for GIMP analysis.	read_idat_zip
Check if GEO ID exists and has IDAT data	validate_geo_dataset