/usr/lib/R/site-library/annotate/INDEX is in r-bioc-annotate 1.56.1+dfsg-1.
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for the ACCNUM environment of a given data
package
GO2heatmap Compute a heatmap for the specified data, for
either a GO category or a KEGG pathway.
GOmnplot A function to plot by group means against each
other.
HTMLPage-class Classes to represent HTML pages
LL2homology DEPRECATED Functions that find the homology
data for a given set of LocusLink ids or
HomoloGeneIDs
PMIDAmat A function to compute the probe to PubMed id
incidence matrix.
PWAmat A function to compute the probe to KEGG pathway
incidence matrix.
UniGeneQuery Create a Query String for a UniGene Identifier
accessionToUID A function to convert accession values to NCBI
UIDs.
annPkgName Get annotation package name from chip name
annotate-defunct Defunct Functions in Package 'annotate'
aqListGOIDs List GO Identifiers by GO Ontology
blastSequences Run a blast query to NCBI for either a string
or an entrez gene ID and then return a series
of MultipleAlignment objects.
buildChromLocation A function to generate an instantiation of a
chromLocation class
buildPubMedAbst A function to generate an instantiation of a
pubMedAbst class
chrCats Returns a list of chromosome locations from a
MAP environment
chromLocation-class Class chromLocation, a class for describing
genes and their chromosome mappings.
compatibleVersions function to check to see if the packages
represented by the names passed have the same
version number
dropECode Drop GO labels for specified Evidence Codes
entrezGeneByID Create a Query String for an Entrez Gene
Identifier
entrezGeneQuery Create a Query String for Entrez Genes
filterGOByOntology Filter GO terms by a specified GO ontology
findNeighbors A function to locate neighboring genes within a
defined range around a target gene represented
by a Entrez Gene ID
genbank A function to open the browser to Genbank with
the selected gene.
getAnnMap Get annotation map
getEvidence Get the Evidence codes for a set of GO terms.
getGOTerm Functions to Access GO data.
getOntology Get GO terms for a specified ontology
getPMInfo extract publication details and abstract from
annotate::pubmed function output
getQueryLink Functions to create hypertext links that can be
placed in a table cell of a HTML file
getSEQ Queries the NCBI database to obtain the
sequence for a given GenBank Accession number
getSYMBOL Functions to deal with Data Packages
hasGOannote Check for GO annotation
hgByChroms A dataset to show the human genome base pair
locations per chromosome.
hgCLengths A dataset which contains the lengths (in base
pairs) of the human chromosomes.
hgu95AProbLocs chromLocation instance hgu95AProbLocs, an
example of a chromLocation object
hgu95Achroloc Annotation data for the Affymetrix HGU95A
GeneChip
hgu95Achrom Annotation data for the Affymetrix HGU95A
GeneChip
hgu95All Annotation data for the Affymetrix HGU95A
GeneChip
hgu95Asym Annotation data for the Affymetrix HGU95A
GeneChip
homoData-class Class "homoData"
htmlpage Functions to build HTML pages
isValidKey Get or verify valid IDs for a package.
makeAnchor A Function To Generate HTML Anchors
mapOrgs Functions to map to organism IDs used by NCBI
homology.
organism Convenience function for getting the organism
from an object or package
p2LL A function to map from probes to unique Entrez
Gene IDs
pm.abstGrep An interface to grep for PubMed abstracts.
pm.getabst Obtain the abstracts for a set PubMed list.
pm.titles Obtain the titles of the PubMed abstracts.
pmAbst2HTML HTML Generation for PubMed Abstracts
pmid2MIAME use web to populate MIAME instance with pubmed
details
pmidQuery A function to query PubMed
pubMedAbst-class Class pubMedAbst, a class to handle PubMed
abstracts, and methods for processing them.
pubmed A function to open the browser to Pubmed with
the selected gene.
readGEOAnn Function to extract data from the GEO web site
serializeEnv A Function To Serialize Environment
setRepository Functions to add arbitrary repositories
updateSymbolsToValidKeys
Take a list of symbols and translate them into
the best possible ID for a package.
usedChromGenes A function to select used genes on a chromosome
from an ExpressionSet.
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