Package: annaffy 1.85.0

Colin A. Smith

annaffy: Annotation tools for Affymetrix biological metadata

Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.

Authors:Colin A. Smith <[email protected]>

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
annaffy/json (API)

# Install 'annaffy' in R:

install.packages('annaffy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

aafExpr - Sample ExpressionSet used for demonstration purposes

On BioConductor:annaffy-1.85.0(bioc 3.24)annaffy-1.84.0(bioc 3.23)

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

onechannel microarray annotation go pathways reportwriting

5.68 score 3 packages 67 scripts 4 mentions 31 exports 37 dependencies

Last updated from:7426eeeb17. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	192
linux-devel-x86_64	WARNING	244
source / vignettes	OK	224
linux-release-x86_64	WARNING	275
macos-release-arm64	WARNING	145
macos-oldrel-arm64	WARNING	164
windows-devel	WARNING	190
windows-release	WARNING	155
windows-oldrel	WARNING	171
wasm-release	OK	160

Exports:aaf.handler aafChromLoc aafChromosome aafCytoband aafDescription aafGenBank aafGO aafLocusLink aafPathway aafProbe aafPubMed aafSearchGO aafSearchText aafSymbol aafTable aafTableAnn aafTableFrame aafTableInt colnames getCSS getHTML getTD getText getURL is.annpkg probeids probeids<-saveHTML saveText selectorWidget show

Dependencies:AnnotationDbi askpass Biobase BiocGenerics BiocManager Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics glue GO.db httr IRanges jsonlite KEGGREST lifecycle memoise mime openssl pkgconfig png R6 rlang RSQLite S4Vectors Seqinfo sys vctrs XVector

annaffy Primer

Loading Annotation Data | Linking to Online Databases | Building HTML Pages | Searching Metadata

Rendered fromannaffy.Rnwusingutils::Sweave

Last update: 2021-01-26
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Handle feching annotation data columns	aaf.handler
Constructor for aafChromLoc objects	aafChromLoc
Class aafChromLoc, a class for gene chromosome locations	aafChromLoc-class
Constructor for aafChromosome objects	aafChromosome
Class aafChromosome, a class for gene chromosome assignments	aafChromosome-class
Constructor for aafCytoband objects	aafCytoband
Class aafCytoband, a class for cytoband data	aafCytoband-class getText,aafCytoband-method getURL,aafCytoband-method show,aafCytoband-method
Constructor for aafDescription objects	aafDescription
Class aafDescription, a class for gene descriptions	aafDescription-class
Sample ExpressionSet used for demonstration purposes	aafExpr
Constructor for aafGenBank objects	aafGenBank
Class aafGenBank, a class for GenBank accession numbers	aafGenBank-class getURL,aafGenBank-method
Constructor for aafGO objects	aafGO
Class aafGO, a class for gene ontology ids	aafGO-class getCSS,aafGO-method getHTML,aafGO-method getTD,aafGO-method getText,aafGO-method getURL,aafGO-method
Class aafGOItem, a class for gene ontology id elements	aafGOItem aafGOItem-class getHTML,aafGOItem-method getText,aafGOItem-method getURL,aafGOItem-method show,aafGOItem-method
Class aafIntensity, a class for gene expression values	aafIntensity aafIntensity-class getTD,aafIntensity-method
Class aafList, a specialized subclass of list	aafList aafList-class getCSS,aafList-method getHTML,aafList-method getTD,aafList-method getText,aafList-method getURL,aafList-method show,aafList-method [,aafList-method
Constructor for aafLocusLink objects	aafLocusLink
Class aafLocusLink, a class for LocusLink ids	aafLocusLink-class getURL,aafLocusLink-method
Constructor for aafPathway objects	aafPathway
Class aafPathway, a class for KEGG pathway ids	aafPathway-class getCSS,aafPathway-method getHTML,aafPathway-method getTD,aafPathway-method getText,aafPathway-method getURL,aafPathway-method
Class aafPathwayItem, a class for KEGG pathway id elements	aafPathwayItem aafPathwayItem-class getHTML,aafPathwayItem-method getText,aafPathwayItem-method getURL,aafPathwayItem-method show,aafPathwayItem-method
Constructor for aafProbe objects	aafProbe
Class aafProbe, a class for Probe ids	aafProbe-class getURL,aafProbe-method
Constructor for aafPubMed objects	aafPubMed
Class aafPubMed, a class for PubMed ids	aafPubMed-class getCSS,aafPubMed-method getHTML,aafPubMed-method getTD,aafPubMed-method getURL,aafPubMed-method
Find probe ids corresponding to GO ids	aafSearchGO
Search metadata annotation text	aafSearchText
Class aafSigned, a class for signed numerical data	aafSigned aafSigned-class getCSS,aafSigned-method getTD,aafSigned-method
Constructor for aafSymbol objects	aafSymbol
Class aafSymbol, a class for gene symbols	aafSymbol-class
Constructor for aafTable objects	aafTable
Class aafTable, a tabular microarray data class	$.aafTable aafTable-class colnames colnames,aafTable-method colnames<- colnames<-,aafTable-method dim.aafTable merge.aafTable probeids probeids,aafTable-method probeids<- probeids<-,aafTable-method rbind.aafTable saveHTML saveHTML,aafTable-method saveText saveText,aafTable-method [,aafTable-method [[,aafTable-method
Constructor for aafTable objects from annotation data	aafTableAnn
Constructor for aafTable objects from data frames	aafTableFrame
Constructor for aafTable objects from ExpressionSets	aafTableInt
Methods for function getCSS	getCSS getCSS,ANY-method getCSS-methods
Methods for function getHTML	getHTML getHTML,ANY-method getHTML-methods
Methods for function getTD	getTD getTD,ANY-method getTD-methods
Methods for function getText	getText getText,ANY-method getText-methods
Methods for function getURL	getURL getURL,ANY-method getURL-methods
Determine if packages contain annotation	is.annpkg
Dialog to select items from a list	selectorWidget