Package index • SigRepo

Connect to Database

newConnHandler(): newConnHandler
conn_init(): conn_init
init_handle(): init_handle
get_handle(): get_handle
clear_handle(): clear_handle

Search Data in Database

searchAssayType(): searchAssayType
searchCollection(): searchCollection
searchKeyword(): searchKeyword
searchOrganism(): searchOrganism
searchPhenotype(): searchPhenotype
searchPlatform(): searchPlatform
searchProteomicsFeatureSet(): searchProteomicsFeatureSet
searchSampleType(): searchSampleType
searchSignature(): searchSignature
searchTranscriptomicsFeatureSet(): searchTranscriptomicsFeatureSet
searchGeneticVariantsFeatureSet(): searchGeneticVariantsFeatureSet
searchMetabolomicsFeatureSet(): searchMetabolomicsFeatureSet
searchUser(): searchUser

Retrieve Data from Database

getAPIKey(): getAPIKey
getCollection(): getCollection
getSignature(): getSignature
getSignatureFeatureSet(): getSignatureFeatureSet

Import Data to Database

addCollection(): addCollection
addKeyword(): addKeyword
addOrganism(): addOrganism
addPhenotype(): addPhenotype
addPlatform(): addPlatform
addProteomicsFeatureSet(): addProteomicsFeatureSet
addProteomicsSignatureSet(): addProteomicsSignatureSet
addMetabolomicsFeatureSet(): addMetabolomicsFeatureSet
addMetabolomicsSignatureSet(): addMetabolomicsSignatureSet
addSampleType(): addSampleType
addSignature(): addSignature
addSignatureToCollection(): addSignatureToCollection
addTranscriptomicsFeatureSet(): addTranscriptomicsFeatureSet
addTranscriptomicsSignatureSet(): addTranscriptomicsSignatureSet
addUser(): addUser
addUserToSignature(): addUserToSignature
addUserToCollection(): addUserToCollection

Update Data in Database

updateCollectionMetadata(): updateCollectionMetadata
updateSignature(): updateSignature
updateUser(): updateUser
updateProteomicsFeatureSet(): updateProteomicsFeatureSet
updateTranscriptomicsFeatureSet(): updateTranscriptomicsFeatureSet

Delete Data from Database

deleteCollection(): deleteCollection
deleteOrganism(): deleteOrganism
deletePhenotype(): deletePhenotype
deletePlatform(): deletePlatform
deleteSampleType(): deleteSampleType
deleteSignature(): deleteSignature
deleteUser(): deleteUser
inActivateUser(): inActivateUser
removeSignatureFromCollection(): removeSignatureFromCollection

Compare Signatures

compareSignatureFeatures(): Compare significant feature overlap between two signatures
compareSignatureScores(): Compare feature score correlation between two signatures
plotSignatureOverlap(): Plot significant feature overlap between two signatures
signatureSetKsTest(): Test enrichment of one signature in another signature's ranked scores

Example Data

Example signatures included in the package

LLFS_Aging_Gene_2023: Transcriptomic signature: Human aging (LLFS cohort, blood, 2023)
Myc_reduce_mice_liver_24m: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-))
omic_signature_1: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-))
omic_signature_2: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-))
omic_signature_3: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-), version 3)
omic_signature_4: Transcriptomic signature: Myc haploinsufficient mouse liver (Myc(+/-), version 4)