Files in pkrog/biodb
Biodb, a Library for Connecting to Chemical and Biological Databases

.Rbuildignore
.gitattributes
.gitignore
.gitmodules
.travis.yml
DESCRIPTION
LICENSE
Makefile
NAMESPACE
R/Biodb.R R/BiodbCache.R R/BiodbChildObject.R R/BiodbCircle.R R/BiodbCompounddbConn.R R/BiodbConfig.R R/BiodbConn.R R/BiodbConnBase.R R/BiodbConnObserver.R R/BiodbCsvEntry.R R/BiodbDbInfo.R R/BiodbDbsInfo.R R/BiodbDownloadable.R R/BiodbEditable.R R/BiodbEntry.R R/BiodbEntryField.R R/BiodbEntryFields.R R/BiodbErrorReporter.R R/BiodbFactory.R R/BiodbHtmlEntry.R R/BiodbInfoReporter.R R/BiodbJsonEntry.R R/BiodbListEntry.R R/BiodbLogger.R R/BiodbMassdbConn.R R/BiodbObject.R R/BiodbObserver.R R/BiodbRect.R R/BiodbRemotedbConn.R R/BiodbRequest.R R/BiodbRequestScheduler.R R/BiodbRequestSchedulerRule.R R/BiodbSdfEntry.R R/BiodbShape.R R/BiodbSqlQuery.R R/BiodbTxtEntry.R R/BiodbUrl.R R/BiodbWarningReporter.R R/BiodbWritable.R R/BiodbXmlEntry.R R/ChebiConn.R R/ChebiEntry.R R/ChemspiderConn.R R/ChemspiderEntry.R R/ExpasyEnzymeConn.R R/ExpasyEnzymeEntry.R R/HmdbMetabolitesConn.R R/HmdbMetabolitesEntry.R R/KeggCompoundConn.R R/KeggCompoundEntry.R R/KeggConn.R R/KeggEntry.R R/KeggEnzymeConn.R R/KeggEnzymeEntry.R R/KeggGenesConn.R R/KeggGenesEntry.R R/KeggModuleConn.R R/KeggModuleEntry.R R/KeggOrthologyConn.R R/KeggOrthologyEntry.R R/KeggPathwayConn.R R/KeggPathwayEntry.R R/KeggReactionConn.R R/KeggReactionEntry.R R/LipidmapsStructureConn.R R/LipidmapsStructureEntry.R R/MassCsvFileConn.R R/MassCsvFileEntry.R R/MassSqliteConn.R R/MassSqliteEntry.R R/MassbankConn.R R/MassbankEntry.R R/MirbaseConn.R R/MirbaseMatureConn.R R/MirbaseMatureEntry.R R/NcbiCcdsConn.R R/NcbiCcdsEntry.R R/NcbiConn.R R/NcbiEntrezConn.R R/NcbiGeneConn.R R/NcbiGeneEntry.R R/NcbiPubchemCompConn.R R/NcbiPubchemCompEntry.R R/NcbiPubchemConn.R R/NcbiPubchemEntry.R R/NcbiPubchemSubstConn.R R/NcbiPubchemSubstEntry.R R/NciCactusConn.R R/NciCactusEntry.R R/PeakforestCompoundConn.R R/PeakforestCompoundEntry.R R/PeakforestConn.R R/PeakforestMassConn.R R/PeakforestMassEntry.R R/UniprotConn.R R/UniprotEntry.R R/biodb-package.R R/mass_helpers.R R/spec-dist.R README.md examples/kegg.compound-search.R examples/massbank-extract.R examples/massbank-ms-search.R examples/massbank-msms-search.R examples/mirbase-tocsv.R
ext/.gitignore
ext/Makefile
ext/tspec.txt
ext/wrapperPeakforest.R
inst/definitions.yml
inst/extdata/lcmsdb.sqlite
inst/extdata/lcmsdb.tsv
inst/extdata/new_entry_field.yml
man/Biodb-class.Rd man/BiodbCache-class.Rd man/BiodbCircle-class.Rd man/BiodbCompounddbConn-class.Rd man/BiodbConfig-class.Rd man/BiodbConn-class.Rd man/BiodbConnBase-class.Rd man/BiodbConnObserver-class.Rd man/BiodbCsvEntry-class.Rd man/BiodbDbInfo-class.Rd man/BiodbDbsInfo-class.Rd man/BiodbDownloadable-class.Rd man/BiodbEditable-class.Rd man/BiodbEntry-class.Rd man/BiodbEntryField-class.Rd man/BiodbEntryFields-class.Rd man/BiodbErrorReporter-class.Rd man/BiodbFactory-class.Rd man/BiodbHtmlEntry-class.Rd man/BiodbInfoReporter-class.Rd man/BiodbJsonEntry-class.Rd man/BiodbListEntry-class.Rd man/BiodbLogger-class.Rd man/BiodbMassdbConn-class.Rd man/BiodbObserver-class.Rd man/BiodbRect-class.Rd man/BiodbRemotedbConn-class.Rd man/BiodbRequest-class.Rd man/BiodbRequestScheduler-class.Rd man/BiodbRequestSchedulerRule-class.Rd man/BiodbSdfEntry-class.Rd man/BiodbShape-class.Rd man/BiodbSqlBinaryOp-class.Rd man/BiodbSqlExpr-class.Rd man/BiodbSqlField-class.Rd man/BiodbSqlList-class.Rd man/BiodbSqlLogicalOp-class.Rd man/BiodbSqlQuery-class.Rd man/BiodbSqlValue-class.Rd man/BiodbTxtEntry-class.Rd man/BiodbUrl-class.Rd man/BiodbWarningReporter-class.Rd man/BiodbWritable-class.Rd man/BiodbXmlEntry-class.Rd man/ChebiConn-class.Rd man/ChebiEntry-class.Rd man/ChemspiderConn-class.Rd man/ChemspiderEntry-class.Rd man/ExpasyEnzymeConn-class.Rd man/ExpasyEnzymeEntry-class.Rd man/HmdbMetabolitesConn-class.Rd man/HmdbMetabolitesEntry-class.Rd man/KeggCompoundConn-class.Rd man/KeggCompoundEntry-class.Rd man/KeggConn-class.Rd man/KeggEntry-class.Rd man/KeggEnzymeConn-class.Rd man/KeggEnzymeEntry-class.Rd man/KeggGenesConn-class.Rd man/KeggGenesEntry-class.Rd man/KeggModuleConn-class.Rd man/KeggModuleEntry-class.Rd man/KeggOrthologyConn-class.Rd man/KeggOrthologyEntry-class.Rd man/KeggPathwayConn-class.Rd man/KeggPathwayEntry-class.Rd man/KeggReactionConn-class.Rd man/KeggReactionEntry-class.Rd man/LipidmapsStructureConn-class.Rd man/LipidmapsStructureEntry-class.Rd man/MassCsvFileConn-class.Rd man/MassCsvFileEntry-class.Rd man/MassSqliteConn-class.Rd man/MassSqliteEntry-class.Rd man/MassbankConn-class.Rd man/MassbankEntry-class.Rd man/MirbaseConn-class.Rd man/MirbaseMatureConn-class.Rd man/MirbaseMatureEntry-class.Rd man/NcbiCcdsConn-class.Rd man/NcbiCcdsEntry-class.Rd man/NcbiConn-class.Rd man/NcbiEntrezConn-class.Rd man/NcbiGeneConn-class.Rd man/NcbiGeneEntry-class.Rd man/NcbiPubchemCompConn-class.Rd man/NcbiPubchemCompEntry-class.Rd man/NcbiPubchemConn-class.Rd man/NcbiPubchemEntry-class.Rd man/NcbiPubchemSubstConn-class.Rd man/NcbiPubchemSubstEntry-class.Rd man/NciCactusConn-class.Rd man/NciCactusEntry-class.Rd man/PeakforestCompoundConn-class.Rd man/PeakforestCompoundEntry-class.Rd man/PeakforestConn-class.Rd man/PeakforestMassConn-class.Rd man/PeakforestMassEntry-class.Rd man/UniprotConn-class.Rd man/UniprotEntry-class.Rd
scripts/.gitignore
scripts/peak-extractor
src/.gitignore
src/closeMatchPpm.c
src/registerDynamicSymbol.c
tests/.gitignore
tests/dockerfiles/conda_install_alpine.dockerfile
tests/dockerfiles/conda_install_centos.dockerfile
tests/dockerfiles/conda_install_ubuntu.dockerfile
tests/res/entry-chebi-15440.json
tests/res/entry-chebi-2528.json
tests/res/entry-chebi-7799.json
tests/res/entry-chemspider-2.json
tests/res/entry-expasy.enzyme-1.1.1.1.json
tests/res/entry-expasy.enzyme-1.1.1.54.json
tests/res/entry-hmdb.metabolites-HMDB0000001.json
tests/res/entry-kegg.compound-C00133.json
tests/res/entry-kegg.compound-C00751.json
tests/res/entry-kegg.enzyme-1.1.1.54.json
tests/res/entry-kegg.enzyme-2.7.1.6.json
tests/res/entry-kegg.genes-mmu%3a14635.json
tests/res/entry-kegg.module-M00009.json
tests/res/entry-kegg.module-M00114.json
tests/res/entry-kegg.orthology-K12668.json
tests/res/entry-kegg.pathway-map00053.json
tests/res/entry-kegg.reaction-R00105.json
tests/res/entry-kegg.reaction-R01528.json
tests/res/entry-kegg.reaction-R01641.json
tests/res/entry-kegg.reaction-R02035.json
tests/res/entry-kegg.reaction-R02736.json
tests/res/entry-lipidmaps.structure-LMFA00000001.json
tests/res/entry-lipidmaps.structure-LMFA00000002.json
tests/res/entry-lipidmaps.structure-LMFA08040013.json
tests/res/entry-mass.csv.file-A10.pos.colzz.5.69.json
tests/res/entry-mass.sqlite-A10.pos.colzz.5.69.json
tests/res/entry-massbank-AU380004.json
tests/res/entry-massbank-EA256108.json
tests/res/entry-massbank-FIO00018.json
tests/res/entry-massbank-KO009087.json
tests/res/entry-massbank-PR010001.json
tests/res/entry-massbank-PR010173.json
tests/res/entry-massbank-PR020137.json
tests/res/entry-massbank.eu-EA256108.json
tests/res/entry-massbank.eu-PR010001.json
tests/res/entry-massbank.eu-PR010173.json
tests/res/entry-mirbase.mature-MIMAT0000433.json
tests/res/entry-mirbase.mature-MIMAT0000434.json
tests/res/entry-ncbi.ccds-CCDS12227.1.json
tests/res/entry-ncbi.ccds-CCDS43240.1.json
tests/res/entry-ncbi.gene-2833.json
tests/res/entry-ncbi.gene-3002.json
tests/res/entry-ncbi.gene-3627.json
tests/res/entry-ncbi.gene-4316.json
tests/res/entry-ncbi.gene-50943.json
tests/res/entry-ncbi.gene-5551.json
tests/res/entry-ncbi.gene-916.json
tests/res/entry-ncbi.gene-9606.json
tests/res/entry-ncbi.pubchem.comp-2.json
tests/res/entry-ncbi.pubchem.comp-65124.json
tests/res/entry-ncbi.pubchem.subst-3.json
tests/res/entry-nci.cactus-749674.json
tests/res/entry-nci.cactus-750690.json
tests/res/entry-peakforest.compound-1839.json
tests/res/entry-peakforest.compound-2075.json
tests/res/entry-peakforest.mass-1000.json
tests/res/entry-peakforest.mass-75.json
tests/res/entry-uniprot-P01011.json
tests/res/entry-uniprot-P02461.json
tests/res/entry-uniprot-P02462.json
tests/res/entry-uniprot-P07911.json
tests/res/entry-uniprot-P08123.json
tests/res/entry-uniprot-P09237.json
tests/res/entry-uniprot-P10480.json
tests/res/entry-uniprot-P60022.json
tests/res/entry-uniprot-Q31611.json
tests/res/mass.csv.file-wrong_header.tsv
tests/res/mass.csv.file-wrong_nb_cols.tsv
tests/res/mass.csv.file.tsv
tests/testthat.R tests/testthat/common.R tests/testthat/db-chebi-tests.R tests/testthat/db-chemspider-tests.R tests/testthat/db-compound-tests.R tests/testthat/db-expasy.enzyme-tests.R tests/testthat/db-generic-tests.R tests/testthat/db-hmdb.metabolites-tests.R tests/testthat/db-kegg.compound-tests.R tests/testthat/db-kegg.enzyme-tests.R tests/testthat/db-kegg.genes-tests.R tests/testthat/db-kegg.module-tests.R tests/testthat/db-kegg.orthology-tests.R tests/testthat/db-kegg.pathway-tests.R tests/testthat/db-kegg.reaction-tests.R tests/testthat/db-lipidmaps.structure-tests.R tests/testthat/db-mass.csv.file-tests.R tests/testthat/db-mass.sqlite-tests.R tests/testthat/db-massbank-tests.R tests/testthat/db-mirbase.mature-tests.R tests/testthat/db-ms-tests.R tests/testthat/db-ncbi.ccds-tests.R tests/testthat/db-ncbi.gene-tests.R tests/testthat/db-ncbi.pubchem.comp-tests.R tests/testthat/db-ncbi.pubchem.subst-tests.R tests/testthat/db-nci.cactus-tests.R tests/testthat/db-peakforest.compound-tests.R tests/testthat/db-peakforest.mass-tests.R tests/testthat/db-uniprot-tests.R tests/testthat/engine-01-abstract-tests.R tests/testthat/engine-05-assertions-tests.R tests/testthat/engine-10-object-printing-tests.R tests/testthat/engine-15-observers-tests.R tests/testthat/engine-20-config-tests.R tests/testthat/engine-30-biodb-tests.R tests/testthat/engine-31-dbinfo-tests.R tests/testthat/engine-50-factory-tests.R tests/testthat/engine-80-scheduler-tests.R tests/testthat/engine-90-shapes-tests.R tests/testthat/engine-99-extension-tests.R tests/testthat/test-00-init.R tests/testthat/test-10-engine.R tests/testthat/test-20-databases.R tests/testthat/test-99.terminate.R
vignettes/.gitignore
vignettes/arch.Rmd vignettes/cactus.Rmd vignettes/chebi.Rmd vignettes/checking_ids.Rmd
vignettes/class-simplified.dia
vignettes/class-simplified.png
vignettes/class.dia
vignettes/class.png
vignettes/class.svg
vignettes/configure.Rmd vignettes/connecting_to_a_db.Rmd vignettes/in_house_lcms_db.Rmd vignettes/in_house_msms_db.Rmd vignettes/init.Rmd vignettes/kegg_pathways.Rmd vignettes/massbank_peaks_extraction.Rmd vignettes/massbank_to_sqlite.Rmd vignettes/merging_entries.Rmd vignettes/new_entry_field.Rmd vignettes/token.Rmd
pkrog/biodb documentation built on Sept. 16, 2019, 3:57 p.m.