Files in thomasp85/FindMyFriends
Microbial Comparative Genomics in R
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS
R/FindMyFriends-package.R
R/RcppExports.R
R/aaa.R
R/constructor.R
R/generics.R
R/ggGraph.R
R/grouping.R
R/investigating.R
R/linearKernel.R
R/linking.R
R/modifying.R
R/pgFull.R
R/pgFullLoc.R
R/pgInMem.R
R/pgInMemLoc.R
R/pgLM.R
R/pgLMLoc.R
R/pgSlim.R
R/pgSlimLoc.R
R/pgVirtual.R
R/pgVirtualLoc.R
R/progress.R
R/similarities.R
R/splitting.R
README.md
inst/extdata/Mycoplasma.zip
inst/extdata/examplePG/example.annot
inst/extdata/examplePG/groupsNS.txt
inst/extdata/examplePG/groupsWG.txt
inst/extdata/examplePG/paraNS.txt
inst/extdata/examplePG/paraWG.txt
man/FindMyFriends-package.Rd
man/addGenomes.Rd
man/addGroupInfo.Rd
man/addOrgInfo.Rd
man/cdhitGrouping.Rd
man/collapseParalogues.Rd
man/defaults.Rd
man/fillDefaults.Rd
man/geneLocation.Rd
man/geneNames.Rd
man/geneWidth.Rd
man/genes.Rd
man/getNeighborhood.Rd
man/getRep.Rd
man/gpcGrouping.Rd
man/graphGrouping.Rd
man/groupInfo.Rd
man/groupNames.Rd
man/groupStat.Rd
man/hasGeneGroups.Rd
man/hasGeneInfo.Rd
man/hasParalogueLinks.Rd
man/internalGroupGenes.Rd
man/internalMergePangenomes.Rd
man/internalMetadata.Rd
man/kmerLink.Rd
man/kmerSimilarity.Rd
man/kmerSplit.Rd
man/loadPgExample.Rd
man/manualGrouping.Rd
man/nGeneGroups.Rd
man/nGenes.Rd
man/nOrganisms.Rd
man/neighborhoodSplit.Rd
man/orgInfo.Rd
man/orgNames.Rd
man/orgStat.Rd
man/pangenome.Rd
man/pcGraph.Rd
man/pgFull-class.Rd
man/pgFullLoc-class.Rd
man/pgInMem-class.Rd
man/pgInMemLoc-class.Rd
man/pgLM-class.Rd
man/pgLMLoc-class.Rd
man/pgMatrix.Rd
man/pgSlim-class.Rd
man/pgSlimLoc-class.Rd
man/pgVirtual-class.Rd
man/pgVirtualLoc-class.Rd
man/plotEvolution.Rd
man/plotGroup.Rd
man/plotNeighborhood.Rd
man/plotSimilarity.Rd
man/plotStat.Rd
man/plotTree.Rd
man/readAnnot.Rd
man/removeGene.Rd
man/reportGroupChanges.Rd
man/seqToGeneGroup.Rd
man/seqToOrg.Rd
man/translated.Rd
man/variableRegions.Rd
src/RcppExports.cpp
src/cdhit-bombs.cpp
src/cdhit-common.cpp
src/cdhit-common.h
src/cdhit-est.cpp
src/cdhit.cpp
src/fastaFunctions.cpp
src/fmf-common.cpp
src/fmf-common.h
src/linearKernel.cpp
src/neighborhoodSim.cpp
src/panSim.cpp
src/progress.cpp
src/progress.h
src/smallgraph.cpp
src/smallgraph.h
tests/testthat.R
tests/testthat/test-GPC.R
tests/testthat/test-addGenomes.R
tests/testthat/test-constructor.R
tests/testthat/test-defaults.R
tests/testthat/test-geneLocation.R
tests/testthat/test-grouping.R
tests/testthat/test-investigating.R
tests/testthat/test-linking.R
tests/testthat/test-loadPgExample.R
tests/testthat/test-modifying.R
tests/testthat/test-orgCompare.R
tests/testthat/test-parallelLinearKernel.R
tests/testthat/test-pgFull.R
tests/testthat/test-pgLM.R
tests/testthat/test-pgSlim.R
tests/testthat/test-similarities.R
tests/testthat/test-splitAndBind.R
tests/testthat/test-splitting.R
vignettes/FindMyFriends_intro.Rmd
vignettes/styles.css
