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protViz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

https://github.com/cpanse/protviz

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 4 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.7%) to scientific vocabulary

Keywords

cran fun mass-spectrometry peptide-identification proteomics quantification rstats visualization
Last synced: 5 months ago · JSON representation

Repository

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Basic Info
Statistics
  • Stars: 11
  • Watchers: 2
  • Forks: 3
  • Open Issues: 6
  • Releases: 3
Topics
cran fun mass-spectrometry peptide-identification proteomics quantification rstats visualization
Created about 11 years ago · Last pushed 9 months ago
Metadata Files
Readme License

README.md

CRAN_Status_Badge codecov

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

{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::packagenativeroutineregistrationskeleton(".", character_only = FALSE)

RcppExport SEXP rcppmodulebootMyModule();

static const RCallMethodDef CallEntries[] = { {"rcppmodulebootMyModule", (DLFUNC) &rcppmodulebootMyModule, 0}, {NULL, NULL, 0} };

RcppExport void RinitminModuleEx(DllInfo *dll) { RregisterRoutines(dll, NULL, CallEntries, NULL, NULL); RuseDynamicSymbols(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

Owner

  • Name: Christian Panse
  • Login: cpanse
  • Kind: user
  • Location: 47N 008E
  • Company: Swiss federal institute of technology in Zurich

proteome informatics; ms comp; visualization; maps; code; reproducible research @hb9feb@fosstodon.org

GitHub Events

Total
  • Push event: 1
  • Pull request event: 1
Last Year
  • Push event: 1
  • Pull request event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 237
  • Total Committers: 4
  • Avg Commits per committer: 59.25
  • Development Distribution Score (DDS): 0.236
Past Year
  • Commits: 8
  • Committers: 1
  • Avg Commits per committer: 8.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Christian Panse cp@f****h 181
Christian Panse c****e 54
Witold Wolski w****i@g****m 1
Grossmann jg@f****h 1
Committer Domains (Top 20 + Academic)
fgcz.ethz.ch: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 18
  • Total pull requests: 3
  • Average time to close issues: 25 days
  • Average time to close pull requests: about 18 hours
  • Total issue authors: 2
  • Total pull request authors: 3
  • Average comments per issue: 0.72
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cpanse (17)
  • HijaziHassan (1)
Pull Request Authors
  • hechth (2)
  • wolski (1)
  • jjGG (1)
Top Labels
Issue Labels
bug (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 536 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 5
  • Total versions: 28
  • Total maintainers: 1
cran.r-project.org: protViz

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

  • Versions: 28
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 536 Last month
Rankings
Dependent repos count: 13.0%
Forks count: 14.2%
Stargazers count: 17.4%
Average: 19.4%
Downloads: 23.7%
Dependent packages count: 28.7%
Maintainers (1)
cp@fgcz.ethz.ch
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1 depends
  • methods * depends
  • Rcpp >= 1.0 imports
  • lattice * suggests
  • testthat * suggests
  • xtable * suggests
.github/workflows/r.yml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r ffe45a39586f073cc2e9af79c4ba563b657dc6e3 composite
inst/Dockerfile docker
  • rocker/rstudio latest build