To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("FindMyFriends")

In most cases, you don't need to download the package archive at all.

FindMyFriends

 

   

Microbial Comparative Genomics in R

Bioconductor version: Release (3.5)

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 gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("http://bioc.ism.ac.jp/biocLite.R")
biocLite("FindMyFriends")

Documentation

HTML R Script Creating pangenomes using FindMyFriends
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, ComparativeGenomics, DataRepresentation, GenomicVariation, GraphAndNetwork, SequenceMatching, Software
Version 1.6.0
In Bioconductor since BioC 3.2 (R-3.2) (1.5 years)
License GPL (>=2)
Depends
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
SystemRequirements
Enhances
URL https://github.com/thomasp85/FindMyFriends
BugReports https://github.com/thomasp85/FindMyFriends/issues
Depends On Me
Imports Me PanVizGenerator
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source FindMyFriends_1.6.0.tar.gz
Windows Binary FindMyFriends_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) FindMyFriends_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/FindMyFriends/tree/release-3.5
Package Short Url http://bioconductor.org/packages/FindMyFriends/
Package Downloads Report Download Stats

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