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README.md 2.20 KiB

Package description

This package provides a range of functions to process and visualize next-generation sequencing data from multi-amplicon sequencing projects. It may work with a range of input variants consisting of a sequence list and count table for these sequences but was initially designed for data generated by the DADA2 package. The functions range from very simple utilities and parsers to complex plotting functions and are packaged as they are here for the convenience of the author and collaborators.

A commented pipeline incorporating most of these functions in the intended sequence can be obtained from the author upon request.

Disclaimer

This R package is under development and intended for use in a specific pipeline, a lot of the functions might not work outside this pipeline/use case. Feel free to inspect and use the code, but don't expect it to be easy or pleasant. The package comes with absolutely no warranty and I take no responsibility for any kind of unintended effects running this code may have.

Documentation of the functions through roxygen-tags and comments was partially assisted by ChatGPT via the awesome chatgpt package by Juan C. Rodriguez. Where documentation was not handwritten by me, I tried to take care to read over the generated text to make sure it's not outright wrong, but some of the help pages might be slightly wonky.

Install

The package can be installed from this GitLab directory with

devtools::install_git("https://gitlab.nibio.no/simeon/campseqr.git")

License: GNU GPL v3

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.