MANTA: Microbial Assemblage Normalized Transcript Analysis (Version 1.22.0)

1 Licensing This package is licensed under the Artistic License v2.0: it is therefore free to use and redistribute, however, we, the copyright holders, wish to maintain primary artistic control over any further development. Please be sure to cite us if you use this package in work leading to publication. Building the manta package from source requires that you have the proper dependency packages, caroline and edgeR, installed from CRAN and Bioconduc-tor respectively. This can typically be accomplished via the following commands from within the R command line environment: install.packages('caroline') # CRAN install biocLite('http://bioconductor.org/biocLite.R') biocLite('edgeR') # Bioconductor install Currently, however, the most recent development version of the edgeR package (> v2.5) is recommended. It must be downloaded from http://bioconductor. org/packages/2.10/bioc/ and built manually. The manta and edgeR packages should be installed from these source archives using the following commands: R CMD INSTALL edgeR_x.y.z.tar.gz R CMD INSTALL manta_x.y.z.tar.gz After a successful installation the manta package can be loaded in the normal way: by starting R and invoking the following library command: > library(manta)