Search for Interesting Gene Sets

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Documentation for package ‘gesel’ version 0.99.5

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

cacheDirectory	Gesel cache directory
consolidateBlockSize	Block size for consolidation
createGeneIdentifierMap	Create mapping of gene identifiers
databaseUrl	Download Gesel database files
downloadDatabaseFile	Download Gesel database files
downloadDatabaseRanges	Fetch byte ranges from a Gesel database file
downloadGeneFile	Fetch Gesel gene annotation files
downloadMultipartRanges	Fetch byte ranges from a Gesel database file
effectiveNumberOfGenes	Effective number of genes
fetchAllCollections	Fetch all gene set collections
fetchAllGenes	Fetch all genes
fetchAllSets	Fetch all gene sets
fetchCollectionSizes	Size of collections
fetchGenesForAllSets	Fetch genes for all sets
fetchGenesForSomeSets	Fetch genes for some sets
fetchGeneTypes	Fetch available gene identfier types
fetchGeneVersion	Fetch version of the gene annotation files
fetchSetsForAllGenes	Fetch sets for all genes
fetchSetsForSomeGenes	Fetch sets for some genes
fetchSetSizes	Size of gene sets
fetchSomeCollections	Fetch some collections
fetchSomeSets	Fetch some sets
findOverlappingSets	Search for overlapping gene sets
flushMemoryCache	Flush the in-memory cache
geneUrl	Fetch Gesel gene annotation files
loadAllSets	Load all gene sets for a species
mapGenesByName	Create mapping of gene identifiers
newConfig	Create a new configuration object
prepareDatabaseFiles	Prepare the Gesel database
prepareGeneFiles	Prepare the Gesel gene annotation files
querySets	Query gene sets
rangeConcurrency	Concurrency of range requests
readDatabaseRanges	Read byte ranges from a Gesel database file
renameGenesInSets	Rename genes in their sets
searchGenes	Search for genes
searchOverlappingSets	Search for overlapping gene sets
searchSetText	Search set text
validateDatabaseFiles	Validate Gesel database files
validateGeneFiles	Validate Gesel database files