eiR: Accelerated similarity searching of small molecules
Version 1.16.0

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Browse man pages Browse package API and functions Browse package files

AuthorKevin Horan, Yiqun Cao and Tyler Backman
Bioconductor views BiomedicalInformatics CellBasedAssays Cheminformatics Clustering DataImport Infrastructure MicrotitrePlateAssay Pharmacogenetics Pharmacogenomics Proteomics Visualization
Date of publicationNone
MaintainerThomas Girke <thomas.girke@ucr.edu>
LicenseArtistic-2.0
Version1.16.0
URL https://github.com/girke-lab/eiR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("eiR")

Man pages

addTransform: Add Transform
eiAdd: Add new compounds
eiCluster: Cluster compounds
eiInit: Initialize a compound database
eiMakeDb: Create an embedded database
eiPerformanceTest: Test the performance of LSH search
eiQuery: Perform a query on an embedded database
example_compounds: Example Compounds
freeLSHData: Deprecated Free LSH Data
loadLSHData: Depreacated Load LSH Data
setDefaultDistance: Set the default distance function for a descriptor type

Functions

IddbVsGivenDist Source code
IddbVsGivenDistBase Source code
IddbVsGivenDistByDescId Source code
IddbVsIddbDist Source code
addTransform Man page Source code
annoySearch Source code
annoySearchAll Source code
buildType Source code
checkEmbedding Source code
compareListsRBO Source code
defaultConn Source code
desc2descDist Source code
descriptorsToCompounds Source code
eiAdd Man page Source code
eiCluster Man page Source code
eiInit Man page Source code
eiMakeDb Man page Source code
eiPerformanceTest Man page Source code
eiQuery Man page Source code
embed Source code
embedAll Source code
embedDescriptor Source code
embedFromRefs Source code
ensureSchema Source code
example_compounds Man page
freeLSHData Man page Source code
genGroupName Source code
genRefName Source code
genRefs Source code
genTestQueryIds Source code
getCompoundGroupId Source code
getCoords Source code
getDefaultDist Source code
getDescriptorIds Source code
getDescriptorType Source code
getDescriptors Source code
getDescriptorsByDescriptorId Source code
getEmbeddedDescriptors Source code
getEmbedding Source code
getEmbeddingId Source code
getExtendedRunInfo Source code
getGroupDescriptorIds Source code
getGroupSize Source code
getNames Source code
getOrCreate Source code
getPreparedQuery Source code
getRun Source code
getRunDescriptorIds Source code
getRunId Source code
getTransform Source code
getUnEmbeddedDescriptorIds Source code
insertEmbeddedDescriptors Source code
insertEmbeddedDescriptorsByCompoundId Source code
insertGroupMembers Source code
invalidateCache Source code
loadLSHData Man page Source code
loadSearchCache Source code
newEmbed Source code
output Source code
readIddb Source code
readIddbFile Source code
readMatrixIndex Source code
readNames Source code
refine Source code
runQuery Source code
search Source code
selectDescriptors Source code
setDefaultConn Source code
setDefaultDistance Man page Source code
testDescriptorSpaceDists Source code
testEmbeddedSpaceDists Source code
testFun Source code
tmessage Source code
toFile Source code
toMatrix Source code
withConnection Source code
writeIddb Source code
writeIddbFile Source code
writeMatrixFile Source code
writeTopN Source code

Files

.BBSoptions
DESCRIPTION
INSTALL
LICENSE
NAMESPACE
R
R/core.R
R/db.R
R/evaluations.R
R/measures.R
README.md
build
build/vignette.rds
data
data/example_compounds.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/eiR.R
inst/doc/eiR.Rmd
inst/doc/eiR.html
inst/schema
inst/schema/data.RPostgreSQL
inst/schema/data.SQLite
inst/unitTests
inst/unitTests/test_main.R
man
man/addTransform.Rd
man/eiAdd.Rd
man/eiCluster.Rd
man/eiInit.Rd
man/eiMakeDb.Rd
man/eiPerformanceTest.Rd
man/eiQuery.Rd
man/example_compounds.Rd
man/freeLSHData.Rd
man/loadLSHData.Rd
man/setDefaultDistance.Rd
src
src/optimFunctions.cc
tests
tests/runTests.R
vignettes
vignettes/Makefile_bootstrap
vignettes/eiR.Rmd
vignettes/eiR.Rmd_bootstrap
vignettes/header.html
vignettes/html.template_bootstrap
vignettes/references.bib
eiR documentation built on May 20, 2017, 10:50 p.m.