Files in ss-lab-cancerunit/SpiderSeqR
A Tool for Integration of Big Bio Data
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/001_Option_Settings.R
R/Accession_Conversion_Functions.R
R/Accession_Functions.R
R/Accession_Search_Functions.R
R/Assembly-helpers.R
R/Assembly.R
R/Console_Messages.R
R/Helper_Functions.R
R/Output_Functions.R
R/Record_Functions.R
R/Search_Anywhere.R
R/Search_Functions.R
R/Simple_Accession_Search_Functions.R
R/SpiderSeqR.R
R/Unifying_Functions.R
R/addMissingSamples.R
R/appendGSEColumns.R
R/chExtractor.R
R/countAccessionMatches.R
R/createFtsTable.R
R/data.R
R/filterByTerm.R
R/getDatabaseInformation.R
R/saExtractor.R
R/searchForAccession.R
R/startSpiderSeqR-Helper_Functions.R
R/startSpiderSeqR.R
R/startSpiderSeqRDemo.R
R/sysdata.rda
R/temp-checkFileDate.R
R/temp.R
R/temp2.R
R/temp3-clearup.R
R/testSpiderSeqRConnections.R
R/utils-pipe.R
README.md
data-raw/Demo_DBs.R
data-raw/SRA_GEO_Category_Conversion.R
data-raw/SRA_GEO_Category_Conversion.csv
data/SRA_GEO_Category_Conversion.rda
data/gse_demo.rda
data/gsm_demo.rda
data/sra_demo.rda
data/srr_demo.rda
man/SRA_GEO_Category_Conversion.Rd
man/SpiderSeqR-package.Rd
man/SpiderSeqREnv.Rd
man/addMissingSamples.Rd
man/classifyAccession.Rd
man/convertAccession.Rd
man/convertCategoriesToLibraryStrategyType.Rd
man/dot-appendGSEColumns.Rd
man/dot-batchedAccSearch.Rd
man/dot-chExtractor.Rd
man/dot-checkCondition.Rd
man/dot-checkDBFile.Rd
man/dot-checkFileDate.Rd
man/dot-checkValidColumns.Rd
man/dot-clearUpDBFiles.Rd
man/dot-convertPairedEnds.Rd
man/dot-countAccessionMatches.Rd
man/dot-createCustomDBFile.Rd
man/dot-createDemoGEO.Rd
man/dot-createDemoSRA.Rd
man/dot-createDemoSRR_GSM.Rd
man/dot-createFtsTable.Rd
man/dot-createMockCustomDB.Rd
man/dot-createMockGEO.Rd
man/dot-createMockSRA.Rd
man/dot-createSpiderMetaInfo.Rd
man/dot-cwt.Rd
man/dot-detectControls.Rd
man/dot-detectInputs.Rd
man/dot-detectMerges.Rd
man/dot-extractGSM.Rd
man/dot-filterSRAByTermByAccessionLevel.Rd
man/dot-findAccessionLevelColumnNames.Rd
man/dot-findDBFiles.Rd
man/dot-findDBFiles_Ori.Rd
man/dot-findFiles.Rd
man/dot-findFiles_Ori.Rd
man/dot-findSRAAccessionLevelColumnNames.Rd
man/dot-generateCallRecord.Rd
man/dot-generateDBExtract.Rd
man/dot-generateEmptyDF.Rd
man/dot-generateFileName.Rd
man/dot-generateFileName_Accession.Rd
man/dot-generateFileName_CALL_SA.Rd
man/dot-generateFileName_CALL_SFA.Rd
man/dot-generateOutput.Rd
man/dot-generateOutput_Accession.Rd
man/dot-generateParameterRecord.Rd
man/dot-generateSampleSheet_ChIP.Rd
man/dot-generateSampleSheet_Other.Rd
man/dot-generateSampleSheet_RNA.Rd
man/dot-generateUniversalSampleSheet.Rd
man/dot-getFurtherDBInfo.Rd
man/dot-listGSEFields.Rd
man/dot-listGSMFields.Rd
man/dot-listSRAFields.Rd
man/dot-manageColumns.Rd
man/dot-manageLibraryStrategy.Rd
man/dot-missingFileCheck.Rd
man/dot-mm.Rd
man/dot-noDBFile.Rd
man/dot-orderDFColumns.Rd
man/dot-parQuery.Rd
man/dot-progressBar.Rd
man/dot-rbindUniqueCols.Rd
man/dot-renameGSEColumns.Rd
man/dot-renameGSMColumns.Rd
man/dot-renameOTHColumns.Rd
man/dot-renameSRAColumns.Rd
man/dot-replaceForbiddenCharacters.Rd
man/dot-saExtractor.Rd
man/dot-searchAnywhereGEO.Rd
man/dot-searchAnywhereGSE.Rd
man/dot-searchAnywhereGSM.Rd
man/dot-searchAnywhereSRA.Rd
man/dot-searchForAccessionAcrossDBsDF.Rd
man/dot-searchForSRPChildren.Rd
man/dot-searchGEOForGSE.Rd
man/dot-searchGEOForGSM.Rd
man/dot-searchSRA.Rd
man/dot-searchSRAForAccession.Rd
man/dot-searchSRR_GSM.Rd
man/dot-setDBConnections.Rd
man/dot-setExpiryParameters.Rd
man/dot-tmenu.Rd
man/dot-unifyDFFormat.Rd
man/dot-unifyNAs.Rd
man/dot-universalExtractor.Rd
man/dot-verifyColumns.Rd
man/dot-verifyConditions.Rd
man/dot-verifyMissingRuns.Rd
man/dot-verifySimpleConditions.Rd
man/dot-verifySuperseries.Rd
man/dot-vex.Rd
man/dot-withOut.Rd
man/dot-writeQuery.Rd
man/dot-writeTableToFile.Rd
man/dot-writeTableToFile_Ori.Rd
man/filterByTerm.Rd
man/filterByTermByAccessionLevel.Rd
man/getColumnDescriptions.Rd
man/getDatabaseInformation.Rd
man/getSpiderSeqROption.Rd
man/gse_demo.Rd
man/gsm_demo.Rd
man/listColumnSets.Rd
man/listValidColumns.Rd
man/orderAccessions.Rd
man/orderDFAccessions.Rd
man/pipe.Rd
man/rerunSpiderSeqR.Rd
man/searchAnywhere.Rd
man/searchForAccession.Rd
man/searchForTerm.Rd
man/selectColumns.Rd
man/selectColumns_Accession.Rd
man/selectColumns_Overview.Rd
man/setSpiderSeqROption.Rd
man/sra_demo.Rd
man/srr_demo.Rd
man/startSpiderSeqR.Rd
man/startSpiderSeqRDemo.Rd
man/testSpiderSeqRConnections.Rd
tests/testthat.R
tests/testthat/setup-xyz.R
tests/testthat/teardown-xyz.R
tests/testthat/test-Accession_Search_Functions.R
tests/testthat/test-Unifying_Functions.R
tests/testthat/test-convertAccession.R
tests/testthat/test-convertCategoriesToLibraryStrategyType.R
tests/testthat/test-manageLibraryStrategy.R
tests/testthat/test-orderAccessions_list.R
tests/testthat/test-orderAccessions_vector.R
tests/testthat/test-setExpiryParameters.R
tests/testthat/test-startSpiderSeqR.R
tests/testthat/test-universalExtractor.R
tests/testthat/test-verifySuperseries.R
tests/testthat/testdata/Mock_Database_Creation.R
tests/testthat/testdata/Mock_Database_Files/All_Present/GEOmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/All_Present/SRAmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/All_Present/SRR_GSM.sqlite
tests/testthat/testdata/Mock_Database_Files/Files_in_Subdirectory/Subdir/GEOmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/Files_in_Subdirectory/Subdir/SRAmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/Files_in_Subdirectory/Subdir/SRR_GSM.sqlite
tests/testthat/testdata/Mock_Database_Files/GEO_Missing/SRAmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/GEO_Missing/SRR_GSM.sqlite
tests/testthat/testdata/Mock_Database_Files/SRA_Missing/GEOmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/SRA_Missing/SRR_GSM.sqlite
tests/testthat/testdata/Mock_Database_Files/SpiderSeqR_Missing/GEOmetadb.sqlite
tests/testthat/testdata/Mock_Database_Files/SpiderSeqR_Missing/SRAmetadb.sqlite
vignettes/.gitignore
vignettes/Quick_SpiderSeqR.Rmd
