decusInLabore/biologicSeqTools2
Seq Analysis Helper Functions

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Man pages for decusInLabore/biologicSeqTools2
Seq Analysis Helper Functions

add2labCatSelectionDBtableadd2labCatSelectionDBtable
add2vecA method
add.category.to.lab.reference.table.hsadd.category.to.lab.reference.table.hs
addCoVarA method
addDGEcomparisons2DesignFileA method
addGeneAnnotationaddGeneAnnotation
addProject2ProjectTableaddProject2ProjectTable
addTPMorFPKMtableaddTPMorFPKMtable
assembleBiologicProjectassembleBiologicProject
assignDbUsersAndPrivilegesassignDbUsersAndPrivileges
bioLOGIC-classbioLOGIC
completeDesignBasedOnSampleIDA method
createAlignmentShellScriptA method
createAnalysisFolderscreateAnalysisFolders
createAndFormatExcelOutputFilesA method
createbulkRNASeqAnalysisBashScriptsA method
createbulkRNASeqAnalysisNFcoreScriptcreatebulkRNASeqAnalysisNFcoreScript
createConcatenateFASTQfilesShellScriptA method
createDdsObjectcreateDdsObject
createDesignFileCrickASFsamplesA method
createExcelWorkbookcreateExcelWorkbook
createGeneNameTablecreateGeneNameTable
create.gmt.file.from.ref.data.tableA method
create.gsea.rnk.filesA method
create.GSEA.tableA method
createNewProjectcreateNewProject
createPCAloadingPlotsA method
createRMDscriptcreateRMDscript
create.rnaseqc.scriptA method
createRNAseqQCscriptA method
createSampleDendrogramA method
createSettingsFilecreateSettingsFile
createSettingsJSONcreateSettingsJSON
createSeuratSettingsFilecreateSeuratSettingsFile
createSRAdownloadScriptcreateSRAdownloadScript
createSRRdownloadScriptcreateSRRdownloadScript
create.timecourse.cat.linescreate.timecourse.cat.lines
create.tpm.and.fpkm.tablesA method
createTrimGaloreShellScriptA method
create.website.parameterscreate.website.parameters
datatable.to.website.ptmA method
dbcat2gmtA method
DGEanalysisDGEanalysis
doDGEanalysisA method
do.differential.expression.analyisA method
doLinearFittingsA method
doLRTanalysisA method
doPCAA method
doQuerydoQuery
DotPlotSBDotPlotSB
excelexcel
hpcClusterSubmisisonA method
import.db.table.from.dbA method
inferDBcategoriesinferDBcategories
killDbConnectionsA method
list.db.table.col.nameslist.db.table.col.names
list.db.tables.in.dblist.db.tables.in.db
listExistingProjectslistExistingProject
loadDESeq2outputFromFileloadDESeq2outputFromFile
LRTanalysisA method
make.hmA method
msigdb.gmt2refDBmsigdb.gmt2refDB
organizeFastqFilesA method
prepareRSEMcountMatrixA method
profileClusterprofileCluster
readAndPrepareCountMatrixA method
retrieve.gene.category.from.dbretrieve.gene.category.from.db
samplesToExcludeFromTSdisplaysampleToExcludeFromTSdisplay
selectHeatmapGenesA method
setAnalysisPathssetAnalysisPaths
setCrickGenomeAndGeneNameTablesetCrickGenomeAndGeneNameTable
setDataBaseParameterssetDataBaseParameters
setGenomeAndGeneNameTablesetGenomeAndGeneNameTable
setMountingPointsetMountingPoint
upload.datatable.to.databaseupload.datatable.to.database
uploadDbTableInfileuploadDbTablInfile
upload.pca.table.to.dbA method
decusInLabore/biologicSeqTools2 documentation built on Nov. 21, 2024, 9:04 p.m.

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