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)
Download the zipped package and unzip it.
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'
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
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.
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!