Files in wanyuac/GeneMates
Analysing association and physical linkage between bacterial genes

.Rbuildignore
.gitattributes
.gitignore
DESCRIPTION
Example/README.md Example/findPhysLink.R
Example/findPhysLink.slurm
Example/lmm.R
Example/lmm.slurm
Example/process_results.R GEMMA/README.md
GEMMA/gemma
GEMMA/manual_v0.96.pdf
GeneMates.Rproj
LICENSE
NAMESPACE
R/func__assignPairID.R R/func__betaSignCongruence.R R/func__calcGeneFreq.R R/func__corCladeProj.R R/func__corPatternProj.R R/func__countAlleles.R R/func__distanceAnalyser__evalPL.R R/func__distanceAnalyser__importPhysicalDists.R R/func__distanceAnalyser__summariseDist.R R/func__distanceAnalyser__summariseDistsForEdges.R R/func__extractPairedRows.R R/func__findMinIncClade.R R/func__findMinIncCladeOfStrains.R R/func__findPhysLink.R R/func__findSeq.R R/func__geoTempAnalyser__calcAllelicDiversityPerCountry.R R/func__geoTempAnalyser__countAllelesPerCountry.R R/func__geoTempAnalyser__countAllelesPerGeneByCountry.R R/func__geoTempAnalyser__countAllelesPerGeneByYear.R R/func__geoTempAnalyser__countAllelesPerYear.R R/func__geoTempAnalyser__getAllelesEarliestAppearance.R R/func__geoTempAnalyser__mkCoocurNetwork.R R/func__geoTempAnalyser__tempNet.R R/func__getAllelesPerPattern.R R/func__getAssocGenePair.R R/func__getGeneClasses.R R/func__getRowsXY.R R/func__importAllelicPAM.R R/func__importCoreGenomeSNPs.R R/func__importGeneticPAM.R R/func__lmm.R R/func__mergeIddAlleles.R R/func__mkFilterTSV.R R/func__networkAnalyser__alleleClusterDistr.R R/func__networkAnalyser__allelicCoMatrix.R R/func__networkAnalyser__compEdgeOccur.R R/func__networkAnalyser__compileGraphs.R R/func__networkAnalyser__countGeneClassLinks.R R/func__networkAnalyser__countNeighbours.R R/func__networkAnalyser__extractSubgraphs.R R/func__networkAnalyser__getClusterMemberCooccurrence.R R/func__networkAnalyser__mkNetwork.R R/func__networkAnalyser__summariseCliques.R R/func__networkAnalyser__summarisePhysDistForClusters.R R/func__networkAnalyser__vertexAttr2Size.R R/func__plr.R R/func__projectSamples.R R/func__retrieveAlleleSetInfo.R R/func__screePlotPCs.R R/func__testForStruEff.R R/func__tree2Clades.R R/func__visualisation__comparePvalues.R R/func__visualisation__drawHeatMap.R R/func__visualisation__heatMapPAM.R R/func__visualisation__ringPlotPAM.R R/func__visualisation__showGeneContent.R R/lib__assoc.R R/lib__distanceAnalyser.R R/lib__envirn.R R/lib__networkAnalyser.R R/lib__visualisation.R README.md
install_GeneMates.sh
man/alleleClusterDistr.Rd man/allelicCoMatrix.Rd man/assignPairID.Rd man/betaSignCongruence.Rd man/calcAllelicDiveristyPerCountry.Rd man/calcGeneFreq.Rd man/compEdgeOccur.Rd man/comparePvalues.Rd man/compileGraphs.Rd man/corCladeProj.Rd man/corPatternProj.Rd man/countAlleles.Rd man/countAllelesPerCountry.Rd man/countAllelesPerGeneByCountry.Rd man/countAllelesPerGeneByYear.Rd man/countAllelesPerYear.Rd man/countGeneClassLinks.Rd man/countNeighbours.Rd man/drawHeatMap.Rd man/evalPL.Rd man/extractPairedRows.Rd man/extractSubgraphs.Rd man/findMinIncClade.Rd man/findMinIncCladeOfStrains.Rd man/findPhysLink.Rd man/findSeq.Rd man/getAllelesEarliestAppearance.Rd man/getAllelesPerPattern.Rd man/getAssocGenePair.Rd man/getClusterMemberCooccurrence.Rd man/getGeneClass.Rd man/getRowsXY.Rd man/heatMapPAM.Rd man/importAllelicPAM.Rd man/importCoreGenomeSNPs.Rd man/importGeneticPAM.Rd man/importPhysicalDists.Rd man/lmm.Rd man/mergeIddAlleles.Rd man/mkCoocurNetwork.Rd man/mkFilterTSV.Rd man/mkNetwork.Rd man/plr.Rd man/projectSamples.Rd man/retrieveAlleleSetInfo.Rd man/ringPlotPAM.Rd man/screePlotPCs.Rd man/showGeneContent.Rd man/summariseCliques.Rd man/summariseDist.Rd man/summariseDistsForEdges.Rd man/summarisePhysDistForClusters.Rd man/tempNet.Rd man/testForStruEff.Rd man/tree2Clades.Rd man/vertexAttr2Size.Rd
wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.