Files in ss-lab-cancerunit/SpiderSeqR

A Tool for Integration of Big Bio Data

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/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 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 vignettes/Quick_SpiderSeqR.Rmd