Installation Instructions

0. Install External Dependencies

The following instructions assume that you have installed R and have installed Xcode (Mac) or Rtools (Windows); as well as Bioconductor.

For Bioconductor, start a fresh R session, and enter the following.

source("http://bioconductor.org/biocLite.R")
biocLite(suppressUpdates = FALSE)
biocLite("ShortRead", suppressUpdates = FALSE)

1. Download and unzip.

Download the zipped package and unzip it.

2. Attempt installation from within R

Start a fresh R session, and enter the following.

install.packages("path/to/dada2",
                 repos = NULL,
                 type = "source",
                 dependencies = c("Depends", "Suggests","Imports"))

For example, if the dada2 source code directory was in ~/github/dada2, then the following would work.

install.packages("~/github/dada2",
                 repos = NULL,
                 type = "source",
                 dependencies = c("Depends", "Suggests","Imports"))

Check Package Version

packageVersion("dada2")
## [1] '0.9.3'

3. Troubleshoot Dependencies (Optional)

At this point, there may be complaints about missing dependencies. To install missing dependencies on either CRAN or Bioconductor, start a fresh R session, and enter the following.

source("http://bioconductor.org/biocLite.R")
biocLite("missing_package_1")
biocLite("missing_package_2")
# ... and so on

4. Re-attempt dada2 Installation

Now once again, after dependencies have been installed.

install.packages("path/to/dada2",
                 repos = NULL,
                 type = "source",
                 dependencies = c("Depends", "Suggests","Imports"))

You should now be done, if installation was successful. If not, do panic, and post a message to the issue tracker.

5. Load Package, Explore Function Documentation

library("dada2")

Now that the package is loaded, look at the help files for the main implemented functions.

help(package="dada2")
?derepFastq
?dada

You are ready to use DADA2!