An R package to process amplicon data
This package has a number of functions to filter, dereplicate and error and
chimera check NGS reads stored in fastq files. From v2.6.0 amplicR
implements a function to process paired end reads (data.proc.paired
). This functionality has not being implemented in the raw2data.proc
wrapper and manual calling of the single functions is needed to carry out the preceding steps in the analytical pipeline. Compatibility of down stream analyses should be preserved, but it has not being. The retained reads after the data processing
described above (or your own reads if you have done this already in another way)
can then be compared against reference
sequences and the number of mismatch is reported. This may be useful when, for
example, screening samples for particular taxa (e.g. a pathogen).
amplicR
is mainly a wrapper of several functions provided by other R packages
in order to automate some common analyses, so if you use it, please make sure to
also cite the relevant packages (these are generally indicated in the
documentation of amplicR
's functions). To find out the correct citation for a
package, you can use the function: citation("package_name")
where you have to
replace package_name with the actual name of the package you are interested
into.
Install the package from version control from within R:
library(devtools)
install_github("carlopacioni/amplicR")
If you have not used devtools
before, then you have to install it with
install.packages("devtools")
If you are on Windows, before loading devtools
, shut down R, download the
Rtools executable file from CRAN webpage and run it.
Note that the Bioconductor packages, which are required dependencies for
amplicR
, are not currently installed along with the package. This may change
in the future, but for now these can be installed (if not installed already)
running the following:
library(amplicR)
setup()
All reasonable care has been taken to ensure that amplicR
functions report the
correct results. However there is no guarantee that the package is bug-free. Also,
amplicR
was developed on a machine running windows 7 and no testing on other OS
has been conducted so far. I can't see any reason why it would not work on linux
or mac, but if in doubt, you may want to replicate the results on a windows
environment.
Use help(amplicR)
?amplicR
or ??amplicR
to see a broad
description of the package. Use help(package = "amplicR")
to see the
documentations available.
Alternatively, a manual is available here
and a tutorial is available here.
If you use amplicR
, please cite: Pending
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