agalmar: A Collection of Tools for Analyzing Agalma Expression Projects

This package contains tools for analyzing phylogenetic and expression projects from Agalma. The interface between Agalma and agalmar is the json file exported from Agalma.

Documentation

See the manual, agalmar-manual.pdf

Example usage

This package comes with a test dataset called janedoe. To process it, you can run:

e <- lapply(janedoe$expression, Expression)

Citing

To find out how to cite hutan, run the following in R:

citation("agalmar")

Installing

From the git repository

First, install the devtools package. Then, run the following in R:

source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")
biocLite("DESeq2")
library(devtools)
install_github('caseywdunn/hutan')
install_github('caseywdunn/agalmar')

Development

This package is built with the excellent devtools (https://github.com/hadley/devtools). Extensive explanations on using devtools to create R packages is available in the book R Packages.

Development typically involves cding to the package directory, launching R, and running some combination of the following:

options(error=traceback) # Get line numbers for errors
library(devtools)
load_all()
test()
document()
check() # A wrapper for R CMD check, see http://r-pkgs.had.co.nz/check.html#check
build() # Create package bundle, including executed vignettes

To regenerate the pdf manual, run the following shell command in the package directory:

R CMD Rd2pdf . --force --output=agalmar-manual.pdf

Funding

This software has been developed with support from the following US National Science Foundation grants:

The evolution of gene expression and functional specialization in Siphonophora (Award Number DEB-1256695)