DOI: 10.18129/B9.bioc.FindMyFriends    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.14 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see FindMyFriends.

Microbial Comparative Genomics in R

Bioconductor version: 3.14

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.

Author: Thomas Lin Pedersen

Maintainer: Thomas Lin Pedersen <thomasp85 at>

Citation (from within R, enter citation("FindMyFriends")):


To install this package, start R (version "4.1") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


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biocViews Clustering, ComparativeGenomics, DataRepresentation, GenomicVariation, GraphAndNetwork, SequenceMatching, Software
Version 1.24.0
In Bioconductor since BioC 3.2 (R-3.2) (6.5 years)
License GPL (>=2)
Imports methods, BiocGenerics, Biobase, tools, dplyr, IRanges, Biostrings, S4Vectors, kebabs, igraph, Matrix, digest, filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro, BiocParallel, utils, stats
LinkingTo Rcpp
Suggests BiocStyle, testthat, knitr, rmarkdown, reutils
Depends On Me
Imports Me PanVizGenerator
Suggests Me
Links To Me
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