decusInLabore/biologicSeqTools
Seq Analysis Helper Functions

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Man pages for decusInLabore/biologicSeqTools
Seq Analysis Helper Functions

add2labCatSelectionDBtableadd2labCatSelectionDBtable
add2vecA method
add.category.to.lab.reference.table.hsadd.category.to.lab.reference.table.hs
addCoVarA method
addDGEcomparisons2DesignFileA method
addGeneAnnotationA method
addProject2ProjectTableaddProject2ProjectTable
addTPMorFPKMtableA method
assignDbUsersAndPrivilegesassignDbUsersAndPrivileges
bioLOGIC-classbioLOGIC
completeDesignBasedOnSampleIDA method
createAlignmentShellScriptA method
createAnalysisFoldersA method
createAndFormatExcelOutputFilesA method
createbulkRNASeqAnalysisBashScriptsA method
createConcatenateFASTQfilesShellScriptA method
createDdsObjectA method
createDesignFileCrickASFsamplesA method
createExcelWorkbookcreateExcelWorkbook
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
DGEanalysisA method
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
LRTanalysisA method
make.hmA method
msigdb.gmt2refDBmsigdb.gmt2refDB
organizeFastqFilesA method
prepareRSEMcountMatrixA method
profileClusterprofileCluster
readAndPrepareCountMatrixA method
retrieve.gene.category.from.dbretrieve.gene.category.from.db
selectHeatmapGenesA method
setAnalysisPathsA method
setCrickGenomeAndGeneNameTableA method
setDataBaseParametersA method
setMountingPointA method
upload.datatable.to.databaseupload.datatable.to.database
uploadDbTableInfileuploadDbTablInfile
upload.pca.table.to.dbA method
decusInLabore/biologicSeqTools documentation built on Jan. 28, 2022, 12:23 p.m.

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