FindMyFriends: Microbial Comparative Genomics in R

A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.

AuthorThomas Lin Pedersen
Date of publicationNone
MaintainerThomas Lin Pedersen <thomasp85@gmail.com>
LicenseGPL (>=2)
Version1.4.0
https://github.com/thomasp85/FindMyFriends

View on Bioconductor

Man pages

addGenomes: Add new organisms to an existing pangenome

addGroupInfo: Safely add group info

addOrgInfo: Safely add organisms info

cdhitGrouping: Gene grouping by preclustering with CD-HIT

collapseParalogues: Merge paralogue gene groups into new gene groups

defaults: Access default values for a pgVirtual subclass object

fillDefaults: Assign object defaults to missing values

FindMyFriends-package: FindMyFriends: Comparative microbial genomics in R

geneLocation: Get gene location for all genes

geneNames: Get and set the names of the genes in the pangenome

genes: Extract gene sequences from a pangenome

geneWidth: Get the sequence length of each gene

getNeighborhood: Extract a graph representation of a gene group neighborhood

getRep: Get a representative sequence for each gene group

gpcGrouping: Guided Pairwise Comparison grouping of genes

graphGrouping: Use igraph to create gene grouping from a similarity matrix

groupInfo: Get and set information about gene group

groupNames: Get and set the names of gene groups in the pangenome

groupStat: Calculate statistics about each gene group

hasGeneGroups: Check whether gene groups are defined

hasGeneInfo: Checks for existance of gene location information

hasParalogueLinks: Checks whether linking of paralogues has been done

internalGroupGenes: Add gene grouping to pangenome

internalMergePangenomes: Merge information from two pangenomes

internalMetadata: Add metadata to the pangenome

kmerLink: Link gene groups by homology

kmerSimilarity: Calculate a similarity matrix based on kmers

kmerSplit: Split gene groups based on similarity

loadPgExample: Load an example pangenome

manualGrouping: Define gene grouping manually

neighborhoodSplit: Split gene groups by neighborhood synteny

nGeneGroups: Get the number of gene groups in a pangenome

nGenes: Get the total number of genes in a pangenome

nOrganisms: Get the number of organisms represented in a pangenome

orgInfo: Get and set information about organisms

orgNames: Get and set the names of organisms in the pangenome

orgStat: Calculate statistics about each organism

pangenome: Construct a pangenome from fasta files

pcGraph: Calculate the panchromosome graph

pgFull-class: Class for in memory pangenome data

pgFullLoc-class: Class for in memory pangenome data with location information

pgInMem-class: FindMyFriends standard base class for pangenomic data

pgInMemLoc-class: Superclass for gene location aware pangenome

pgLM-class: Class for reference based pangenome data

pgLMLoc-class: Class for reference based pangenome data with location...

pgMatrix: Get the pangenome matrix

pgSlim-class: Class for pangenome data with no reference to genes

pgSlimLoc-class: Class for pangenome data with no reference to genes

pgVirtual-class: Base class for pangenomic data

pgVirtualLoc-class: Superclass for gene location aware pangenome

plotEvolution: Plot the evolution in gene groups

plotGroup: Plot the similarities of genes within a group

plotNeighborhood: Plot the neighborhood of a gene group

plotSimilarity: Create a heatplot with similarities between all organisms

plotStat: Plot (very) basic statistics on the pangenome

plotTree: Plot a dendrogram of the organisms in a pangenome

readAnnot: Import annotation from an .annot file

removeGene: Remove genes from a pangenome

reportGroupChanges: Reports the change in grouping

seqToGeneGroup: Get gene-to-genegroup relationship

seqToOrg: Get gene-to-organism relationship

translated: Check the sequence type of the pangenome

variableRegions: Detect regions of high variability in the panchromosome

Files in this package

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

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