Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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. 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.


Documentation

The package ships with two pdf vignettes.

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/protViz/protViz', build_vignettes = TRUE, quiet = FALSE)
library(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.

Related approaches

Research software impact

News

BUG FIXES

o free memory computeFragmentIons.c

INSTALL

o added more tests for deisotoper.R and fragmentIon.R

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("protViz")

0.3.1 by Christian Panse, a month ago


https://github.com/protViz/protViz/


Report a bug at https://github.com/protViz/protViz/issues


Browse source code at https://github.com/cran/protViz


Authors: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>), Jonas Grossmann [aut] (<https://orcid.org/0000-0002-6899-9020>), Simon Barkow-Oesterreicher [ctb]


Documentation:   PDF Manual  


GPL-3 license


Imports Rcpp

Depends on methods

Suggests lattice, RUnit, xtable

Linking to Rcpp

System requirements: C++11


Suggested by deisotoper.


See at CRAN