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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("FindMyFriends")
In most cases, you don't need to download the package archive at all.
FindMyFriends
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see FindMyFriends.
Microbial Comparative Genomics in R
Bioconductor version: 3.2
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("https://bioconductor.org/biocLite.R")
biocLite("FindMyFriends")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("FindMyFriends")
| HTML | Creating pangenomes using FindMyFriends | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, ComparativeGenomics, DataRepresentation, GenomicVariation, GraphAndNetwork, SequenceMatching, Software |
| Version | 1.0.7 |
| In Bioconductor since | BioC 3.2 (R-3.2) (0.5 years) |
| License | GPL (>=2) |
| Depends | |
| Imports | methods, Biobase, tools, dplyr, IRanges, Biostrings, S4Vectors, kebabs, igraph, Matrix, digest, filehash, Rcpp, ggplot2, gtable, grid, reshape2, ggdendro, BiocParallel |
| LinkingTo | Rcpp |
| Suggests | testthat, knitr, rmarkdown, reutils |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/thomasp85/FindMyFriends |
| BugReports | https://github.com/thomasp85/FindMyFriends/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | FindMyFriends_1.0.7.tar.gz |
| Windows Binary | FindMyFriends_1.0.7.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | FindMyFriends_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | FindMyFriends_1.0.7.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/FindMyFriends/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/FindMyFriends/ |
| Package Downloads Report | Download Stats |
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