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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Support for KbaseKit for MG-RAST interface #94

Closed joey711 closed 10 years ago

joey711 commented 12 years ago

Although in preliminary stage and no official release, KbaseKit will provide a way to import data directly from MG-RAST in R.

MG-RAST: http://metagenomics.anl.gov/

The development repository is on GitHub. I also forked a version, but this should probably be re-forked as it is under heavy development.

https://github.com/MG-RAST/matR

Installation of KbaseKit:

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("pcaMethods")

# Install directly from GitHub: "KbaseKit"
library(devtools)
install_github("matR", "MG-RAST")
joey711 commented 10 years ago

MG-RAST has not released an official R package as an API, and they do export to BIOM format. For now it would seem this issue is moot, unless someone can point out a specific unsupported step that would be useful.