Package: affycoretools 1.79.0

James W. MacDonald

affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.

Authors:James W. MacDonald

affycoretools_1.79.0.tar.gz
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affycoretools.pdf |affycoretools.html✨
affycoretools/json (API)
NEWS

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

Peer review:

On BioConductor:affycoretools-1.79.0(bioc 3.21)affycoretools-1.78.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

reportwritingmicroarrayonechannelgeneexpression

6.56 score 1 packages 122 scripts 804 downloads 36 mentions 25 exports 188 dependencies

Last updated 2 months agofrom:b82bcab95d. Checks:OK: 1 NOTE: 6. Indexed: yes.

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

Exports:affyLinksaffystartannotateEsetdoGlimmaensemblLinksentrezLinksgetMainProbesgoLinksmakeGoTablemakeHmapmakeImagesmakeVennmaplotmirna2mrnanuccoreLinksoutputRomerplotDegplotHistplotPCArunRomervennCounts2vennInLinevennPagevennSelect2writeFit

Dependencies:abindaffyaffyioannotateAnnotationDbiAnnotationFilterAnnotationForgeaskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemCategorycaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2dichromatdigestdplyredgeRensembldbevaluatefansifarverfastmapfffilelockfontawesomeforcatsforeachforeignformatRFormulafsfutile.loggerfutile.optionsgcrmagenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGGallyggbioggplot2ggstatsGlimmaglueGO.dbGOstatsgplotsgraphgridExtraGSEABasegtablegtoolshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2hwriterIRangesisobanditeratorsjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetoligoClassesopensslOrganismDbipatchworkPFAM.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogressProtGenericspurrrR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlReportingToolsreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioc

Creating annotated output with \Biocpkg{affycoretools} and ReportingTools

James W. MacDonald

Rendered fromRefactoredAffycoretools.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2018-02-02
Started: 2017-11-15

Readme and manuals

Help Manual

Help pageTopics
Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.affycoretools
Pre-processing for Affymetrix Dataaffystart
Method to annotate ExpressionSets automaticallyannotateEset annotateEset,ExpressionSet,AffyExonPDInfo-method annotateEset,ExpressionSet,AffyExpressionPDInfo-method annotateEset,ExpressionSet,AffyGenePDInfo-method annotateEset,ExpressionSet,AffyHTAPDInfo-method annotateEset,ExpressionSet,character-method annotateEset,ExpressionSet,ChipDb-method annotateEset,ExpressionSet,data.frame-method
A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data.dataAndHeatmapPage
A function to generate MA-plots from Glimma, for all contrasts.doGlimma
Add links to data when using ReportingToolsaffyLinks ensemblLinks entrezLinks goLinks nuccoreLinks
Fix data.frame header for use with ReportingToolsfixHeaderAndGo
A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set.geneSetPage
Remove control probesets from ST arraysgetMainProbes
A function to create a simple heatmap and key.gsHeatmap
Make Gene table from GO analysis resultsmakeGoGeneTable
Create HTML tables for Gene Ontology (GO) analysesmakeGoTable
A function to create a heatmap-like object or matrix of correlations between miRNA and mRNA data.makeHmap
Add dotplot imagesmakeImages
High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.makeVenn makeVenn,DGEGLM-method makeVenn,MArrayLM-method
A Function to make MA plots from all arrays.maplot
A function to map miRNA to mRNA.mirna2mrna
A function to create HTML output from the results of running romer on a set of contrasts.outputRomer outputRomer,DGEList,DGEGLM-method outputRomer,EList,MArrayLM-method outputRomer,ExpressionSet,MArrayLM-method
Functions to Plot Density and RNA Degradation PlotsplotDeg plotHist
A Function to Make a PCA Plot from an ExpressionSet or matrixplotPCA plotPCA,ExpressionSet-method plotPCA,matrix-method
A function to run the romer function on a set of contrasts.runRomer runRomer,DGEList-method runRomer,EList-method runRomer,ExpressionSet-method
4-way Venn Diagramsvenn4Way
Compute Counts for Venn DiagramvennCounts2
Generate Venn diagrams with links for Rmarkdown documentsvennInLine
High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes.vennPage
Select and Output Genelists Based on Venn DiagramsvennSelect2
Function to output annotated fit data from limmawriteFit