Package: gesel 0.99.3

Aaron Lun

gesel: Search for Interesting Gene Sets

Query the gesel indices to identify interesting gene sets. Users can test for enrichment in their own list of genes and/or search by text in the set names or descriptions. The indices can be hosted remotely or on a local filesystem.

Authors:Aaron Lun [aut, cre]

gesel_0.99.3.tar.gz
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gesel_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gesel/json (API)
NEWS

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

Bug tracker:https://github.com/gesel-inc/gesel-r/issues

Uses libs:
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

genesetenrichmentdataimportpathwayszlibcpp

2.60 score 39 exports 16 dependencies

Last updated from:a595854f31. Checks:5 WARNING, 8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING151
linux-devel-arm64ERROR255
linux-devel-x86_64ERROR406
source / vignettesERROR277
linux-release-arm64WARNING265
linux-release-x86_64WARNING374
macos-release-arm64ERROR269
macos-release-x86_64ERROR269
macos-oldrel-arm64WARNING259
macos-oldrel-x86_64WARNING310
windows-develERROR260
windows-releaseERROR201
windows-oldrelERROR255
wasm-releaseOK122

Exports:cacheDirectoryconsolidateBlockSizecreateGeneIdentifierMapdatabaseUrldownloadDatabaseFiledownloadDatabaseRangesdownloadGeneFiledownloadMultipartRangeseffectiveNumberOfGenesfetchAllCollectionsfetchAllGenesfetchAllSetsfetchCollectionSizesfetchGenesForAllSetsfetchGenesForSomeSetsfetchGeneTypesfetchGeneVersionfetchSetsForAllGenesfetchSetsForSomeGenesfetchSetSizesfetchSomeCollectionsfetchSomeSetsfindOverlappingSetsflushMemoryCachegeneUrlloadAllSetsmapGenesByNamenewConfigprepareDatabaseFilesprepareGeneFilesquerySetsrangeConcurrencyreadDatabaseRangesrenameGenesInSetssearchGenessearchOverlappingSetssearchSetTextvalidateDatabaseFilesvalidateGeneFiles

Dependencies:askpassassortheadclicurlgluehttr2lifecyclemagrittropensslR6rappdirsRcpprlangsysvctrswithr

Readme and manuals

Help Manual

Help pageTopics
Gesel cache directorycacheDirectory
Block size for consolidationconsolidateBlockSize
Create mapping of gene identifierscreateGeneIdentifierMap mapGenesByName
Download Gesel database filesdatabaseUrl downloadDatabaseFile
Fetch byte ranges from a Gesel database filedownloadDatabaseRanges downloadMultipartRanges
Fetch Gesel gene annotation filesdownloadGeneFile geneUrl
Effective number of geneseffectiveNumberOfGenes
Fetch all gene set collectionsfetchAllCollections
Fetch all genesfetchAllGenes
Fetch all gene setsfetchAllSets
Size of collectionsfetchCollectionSizes
Fetch genes for all setsfetchGenesForAllSets
Fetch genes for some setsfetchGenesForSomeSets
Fetch available gene identfier typesfetchGeneTypes
Fetch version of the gene annotation filesfetchGeneVersion
Fetch sets for all genesfetchSetsForAllGenes
Fetch sets for some genesfetchSetsForSomeGenes
Size of gene setsfetchSetSizes
Fetch some collectionsfetchSomeCollections
Fetch some setsfetchSomeSets
Flush the in-memory cacheflushMemoryCache
Load all gene sets for a speciesloadAllSets
Create a new configuration objectnewConfig
Prepare the Gesel databaseprepareDatabaseFiles
Prepare the Gesel gene annotation filesprepareGeneFiles
Query gene setsquerySets
Concurrency of range requestsrangeConcurrency
Read byte ranges from a Gesel database filereadDatabaseRanges
Rename genes in their setsrenameGenesInSets
Search for genessearchGenes
Search for overlapping gene setsfindOverlappingSets searchOverlappingSets
Search set textsearchSetText
Validate Gesel database filesvalidateDatabaseFiles validateGeneFiles