FindMyFriends

This package is for version 3.12 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: 3.12

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 (version "4.0") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("FindMyFriends")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("FindMyFriends")
Creating pangenomes using FindMyFriends HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, ComparativeGenomics, DataRepresentation, GenomicVariation, GraphAndNetwork, SequenceMatching, Software
Version 1.20.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 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
System Requirements
URL https://github.com/thomasp85/FindMyFriends
Bug Reports https://github.com/thomasp85/FindMyFriends/issues
See More
Suggests BiocStyle, testthat, knitr, rmarkdown, reutils
Linking To Rcpp
Enhances
Depends On Me
Imports Me PanVizGenerator
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package FindMyFriends_1.20.0.tar.gz
Windows Binary FindMyFriends_1.19.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) FindMyFriends_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/FindMyFriends
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/FindMyFriends
Bioc Package Browser https://code.bioconductor.org/browse/FindMyFriends/
Package Short Url https://bioconductor.org/packages/FindMyFriends/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.12 Source Archive