https://github.com/cpanse/protviz
Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
https://github.com/cpanse/protviz
cran fun mass-spectrometry peptide-identification proteomics quantification rstats visualization
Last synced: 5 months ago
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Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
- Host: GitHub
- URL: https://github.com/cpanse/protviz
- Owner: cpanse
- License: gpl-3.0
- Created: 2014-12-04T06:02:13.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2023-12-14T11:11:49.000Z (over 1 year ago)
- Last Synced: 2024-03-14T18:18:45.025Z (about 1 year ago)
- Topics: cran, fun, mass-spectrometry, peptide-identification, proteomics, quantification, rstats, visualization
- Language: R
- Homepage: https://CRAN.R-project.org/package=protViz
- Size: 2.42 MB
- Stars: 10
- Watchers: 3
- Forks: 3
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://cran.r-project.org/package=protViz)
[](https://cran.r-project.org/package=protViz)
[](https://cran.r-project.org/package=protViz)
[](https://app.codecov.io/github/cpanse/protViz)
# 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](https://github.com/cpanse/protViz)
install the latest development version
```{r}
install.packages('devtools')
library(devtools)
install_git('https://github.com/cpanse/protViz', build_vignettes = FALSE, quiet = FALSE)
library(protViz)
```
or
```{r}
BiocManager::install('cpanse/protViz')
```
### R CMD build hints
```{r}
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](https://CRAN.R-project.org/package=protViz) page.
## Related approaches
* [RforProteomics](https://bioconductor.org/packages/RforProteomics/)
* [Spectra](https://github.com/rformassspectrometry/Spectra)