About Pavian
Pavian is a web application for exploring metagenomics classification results, with a special focus on infectious disease diagnosis. Pinpointing pathogens in metagenomics classification results is often complicated by host and laboratory contaminants as well as many non-pathogenic microbiota. With Pavian, researchers can analyze, display and transform results from the Kraken and Centrifuge classifiers using interactive tables, heatmaps and flow diagrams. Pavian also provides an alignment viewer for validation of matches to a particular genome.
Source code and most up-to-date documentation is available at https://github.com/fbreitwieser/pavian.
Preprint now available at http://biorxiv.org/content/early/2016/10/31/084715.full.pdf html.
Installing and running Pavian
In R / RStudio:
## Installs required packages from CRAN and Bioconductor
source("https://raw.githubusercontent.com/fbreitwieser/pavian/master/inst/shinyapp/install-pavian.R")
pavian::runApp(port=5000)
## The above command no longer works in R Studio (as of 2020). Try this instead:
install.packages("remotes")
remotes::install_github("fbreitwieser/pavian")
pavian::runApp(port=5000)
With Docker:
docker run -p 5000:80 florianbw/pavian
In both cases Pavian will be available at http://127.0.0.1:5000 .
Authors/Contributors
Florian Breitwieser (
fbreitw1 jhmi edu
)
Steven Salzberg
