FindMyFriends
This package is for version 3.9 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: 3.9
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>
citation("FindMyFriends")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Clustering, ComparativeGenomics, DataRepresentation, GenomicVariation, GraphAndNetwork, SequenceMatching, Software |
| Version | 1.14.0 |
| 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_1.14.0.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 |
| 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 3.9 | Source Archive |