RosetteDetector

An R package for detecting annd measuring size of Arabidopsis rosettes.

Uses a Support Vector Machine to find the plant.

Visit the package’s website.

Installation

It is also recommended that you install the R package devtools. Just launch R and type:

install.packages("devtools")

Once you have devtools installed, you can install with:

devtools::install_github("surh/RosetteDetector/")

Development version

For the development version, one must switch to the dev branch.

devtools::install_github("surh/RosetteDetector/", ref='dev')

Dependencies

The full list of dependencies is specified in the “Imports” and “Suggests” fields of the DESCRIPTION file.

R should automatically pull and install all the dependencies that are on CRAN. You can also manually install them with the base R function install.packages.

EBImage must be installed via bioconductor and you can find installation instructions that package’s website. Typically you would type the following in the R prompt:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("EBImage")

Usage

For a basic introduction to the usage. Please look at the basic pipeline vignette.

If you have already installed the package you can use the following command in the R prompt:

vignette('pipeline', package = 'RosetteDetector')

You can also find where the vignette was installed in your system by typing:

system.file("doc",package = "RosetteDetector", mustWork = TRUE)

Referencing

For referencing please use the version doi.

Copyright & license

(C) Copyright 2017-2018 Sur Herrera Paredes

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.