FindMyFriends

DOI: 10.18129/B9.bioc.FindMyFriends    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see FindMyFriends.

Microbial Comparative Genomics in R

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Clustering, ComparativeGenomics, DataRepresentation, GenomicVariation, GraphAndNetwork, SequenceMatching, Software
Version	1.14.0
In Bioconductor since	BioC 3.2 (R-3.2) (4 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
Links To Me
Build Report

Package Archives

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

Source Package	FindMyFriends_1.14.0.tar.gz
Windows Binary	FindMyFriends_1.14.0.zip
Mac OS X 10.11 (El Capitan)	FindMyFriends_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/FindMyFriends
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/FindMyFriends
Package Short Url	https://bioconductor.org/packages/FindMyFriends/
Package Downloads Report	Download Stats