GIMP/NAMESPACE at main · SAADAT-Abu/GIMP · GitHub

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export(GIMP_app)
export(ICRs_heatmap)
export(calculate_detection_pvalues)
export(check_minfi_functions)
export(create_bedmeth)
export(create_sample_sheet_template)
export(iDMPs)
export(make_ICRs)
export(make_cpgs)
export(plot_cpgs_coverage)
export(plot_line_ICR)
export(preview_idat_zip)
export(read_idat_zip)

# New GEO-related exports
export(validate_geo_dataset)
export(process_geo_dataset)
export(diagnose_geo_dataset)
export(get_geo_phenotype_data)
export(process_geo_with_mappings)

import(BiocManager)
import(shiny)
import(BiocParallel)
import(R.utils)
import(dplyr)
import(tidyr)
import(tibble)
importFrom(DT, datatable)
importFrom(limma, lmFit)
importFrom(limma, eBayes)
importFrom(limma, topTable)
import(shinydashboard)
importFrom(dplyr, full_join)
importFrom(tibble, rownames_to_column)
importFrom(tibble, column_to_rownames)
importFrom(dplyr, summarise_all)
importFrom(dplyr, across)
importFrom(dplyr, summarize)
importFrom(dplyr, n)
importFrom(tidyr, replace_na)
importFrom(tidyr, pivot_longer)
importFrom(ggplot2, ggplot)
importFrom(ggplot2, aes)
importFrom(ggplot2, geom_bar)
importFrom(ggplot2, geom_line)
importFrom(ggplot2, geom_point)
importFrom(ggplot2, geom_rug)
importFrom(ggplot2, geom_vline)
importFrom(ggplot2, position_dodge)
importFrom(ggplot2, labs)
importFrom(ggplot2, theme)
importFrom(ggplot2, theme_bw)
importFrom(ggplot2, theme_minimal)
importFrom(ggplot2, element_text)
importFrom(ggplot2, element_line)
importFrom(ggplot2, scale_color_manual)
importFrom(ggplot2, scale_y_continuous)
importFrom(ggplot2, coord_flip)
importFrom(ggplot2, ylim)
import(valr)
import(readr)
import(viridisLite)
import(ggplotify)
import(plotly)
import(doParallel)
import(IlluminaHumanMethylation450kanno.ilmn12.hg19)
import(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
import(IlluminaHumanMethylationEPICv2anno.20a1.hg38)
import(IlluminaHumanMethylation450kmanifest)
import(IlluminaHumanMethylationEPICmanifest)
import(IlluminaHumanMethylationEPICv2manifest)
import(minfi)
import(pheatmap)

# GEO-related imports
importFrom(GEOquery, getGEO)
importFrom(GEOquery, getGEOSuppFiles)
importFrom(GEOquery, GSMList)
importFrom(GEOquery, Meta)
importFrom(Biobase, pData)

# Existing imports
importFrom(minfi, read.metharray.exp)
importFrom(minfi, getBeta)
importFrom(minfi, preprocessQuantile)
importFrom(minfi, preprocessSWAN)
importFrom(minfi, preprocessFunnorm)
importFrom(minfi, preprocessNoob)
importFrom(minfi, getGreen)
importFrom(minfi, getRed)
importFrom(minfi, getProbeInfo)
importFrom(utils, unzip)
importFrom(utils, read.csv)
importFrom(utils, untar)
importFrom(utils, zip)
importFrom(utils, data)
importFrom(utils, head)
importFrom(utils, installed.packages)
importFrom(utils, packageVersion)
importFrom(utils, write.csv)
importFrom(stats, complete.cases)
importFrom(stats, median)
importFrom(stats, quantile)
importFrom(stats, sd)
importFrom(stats, end)
importFrom(stats, model.matrix)
importFrom(stats, na.omit)
importFrom(stats, relevel)
importFrom(stats, reorder)
importFrom(stats, setNames)
importFrom(stats, start)
importFrom(stats, var)
importFrom(grDevices, colorRampPalette)
importFrom(tools, file_ext)
importFrom(readxl, read_excel)
importFrom(parallel, detectCores)