Description
Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics.
Description
Helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do data analysis for small scale data sets.
README.md
protViz - Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
Documentation
The package ships with two pdf vignettes.
browseVignettes('protViz')
vignette('protViz')
vignette('PTM_MarkerFinder')
Installation
CRAN
install.packages('protViz')
from github
install the latest development version
install.packages('devtools')
library(devtools)
install_git('https://github.com/cpanse/protViz', build_vignettes = FALSE, quiet = FALSE)
library(protViz)
or
BiocManager::install('cpanse/protViz')
R CMD build hints
Rcpp::compileAttributes()
tools::package_native_routine_registration_skeleton(".", character_only = FALSE)
RcppExport SEXP _rcpp_module_boot_MyModule();
static const R_CallMethodDef CallEntries[] = {
{"_rcpp_module_boot_MyModule", (DL_FUNC) &_rcpp_module_boot_MyModule, 0},
{NULL, NULL, 0}
};
RcppExport void R_init_minModuleEx(DllInfo *dll) {
R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
R_useDynamicSymbols(dll, FALSE);
}
Docker
docker pull cpanse/protviz \
&& docker run -d -p 8792:8787 cpanse/protviz
connect to http://yourdockerhost:8791 using a web browser
- username: rstudio
- password: rstudio
Documentation
The package ships with a package vignette (browseVignettes('protViz') and a reference manual (just type ?protViz on the R shell).
Both documents are also available on the package's CRAN page.