KoinaR

Installation

We are currently waiting for KoinaR to be accepted into bioconductor until then you can install the package directly from github. To do that you will need to install devtools install.packages('devtools').

Install KoinaR by running devtools::install_github('wilhelm-lab/koinar')

Usage

input <- data.frame(
  peptide_sequences = c("LGGNEQVTR", "GAGSSEPVTGLDAK"),
  collision_energies = c(25, 25),
  precursor_charges = c(1, 2)
)

prosit2019 <- koinar::Koina$new(
  model_name = "Prosit_2019_intensity",
  server_url = "koina.wilhelmlab.org:443"
)

prediction_results <- prosit2019$predict(input)

Contribute

Setup dependencies

I recommend using the rocker/rstudio docker container for development.

docker run \
  -p 8888:8787 \
  -d \
  --name rstudio_server \
  -v $HOME:/workspace \
  -e PASSWORD=password \
  -e USERID=$(id -u) \
  -e GROUPID=$(id -g) \
  rocker/rstudio:latest

install.packages(c("roxygen2", "BiocManager", "httr", "jsonlite", "rmarkdown", "testthat", "pdflatex", "protViz", "OrgMassSpecR"))
BiocManager::install(c('BiocStyle', 'BiocCheck', 'Spectra', 'msdata'))

Dependencies to build vignette with Knit

apt update
apt-get install texlive-latex-base texlive-fonts-extra mono-runtime zlib1g-dev libnetcdf19

Build documentation

Use roxygen2 to create documentation based on inline comments. roxygen2::roxygenise().

Run tests

We use testthat to run tests. In the build tab in Rstudio click on Test. Make sure you installed the package beforehand by clicking Install in the build tab.

Verify code style

Verify code style according to bioconductor guidelines. BiocCheck::BiocCheck()