Skip to content

SebastianDall/ampvis2

This branch is 88 commits behind KasperSkytte/ampvis2:main.

Folders and files

NameName
Last commit message
Last commit date
Jan 6, 2022
Jan 7, 2022
Aug 19, 2021
Aug 3, 2020
Jan 7, 2022
Jan 6, 2022
Nov 25, 2021
Jan 6, 2022
May 2, 2017
Jul 7, 2021
Jan 6, 2022
Nov 25, 2021
Apr 20, 2018
Jun 15, 2018
Jan 5, 2022
Nov 25, 2021
Jan 7, 2022
Jul 6, 2021

Repository files navigation

R-CMD-check

Tools for visualising amplicon data

ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.

Installing ampvis2

First, install R (3.5.x or later) and RStudio. Windows users should also install RTools. Then open RStudio as administrator (!) and run the commands below to install ampvis2 from the console:

install.packages("remotes")
remotes::install_github("MadsAlbertsen/ampvis2")

Tip: For faster installation you can utilise multicore processors by setting the Ncpus argument, fx remotes::install_github("madsalbertsen/ampvis2", Ncpus = 6). Most CPU's today can run 8 processes simultaneously, so setting it to 6 is a good starting point unless you know you have a CPU with more (logical) cores than 8.

Get started

For a quick guide on how to use ampvis2 go to the Get Started page. Detailed documentation of all ampvis2 functions can be found at the Functions page.

RStudio Docker container

A Docker container based on the rocker/rstudio image is also provided with ampvis2 preinstalled. This is ideal for complete reproducibility and portability. All you need to do is install Docker and then run:

docker run -d \
  -e "PASSWORD=supersafepassword" \
  -v "local/folder/to/mount":/home/rstudio \
  -p 8787:8787 \
  ghcr.io/madsalbertsen/ampvis2:main

Access RStudio server through a browser at http://localhost:8787 with username rstudio. Ideally use a specific version tag, fx v2.7.12, instead of main to not just pull the latest image every time.

Blog posts about ampvis2

Check out the blog posts at http://albertsenlab.org/ about selected ampvis2 plotting functions. The posts include details as well as example code:

Shiny app

An interactive Shiny app with some of the basic functionality of ampvis2 can be found at: https://kasperskytte.shinyapps.io/shinyampvis

About

Tools for visualising amplicon data

Resources

License

Citation

Stars

Watchers

Forks

Packages

No packages published

Languages

  • R 99.5%
  • Dockerfile 0.5%