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topdownr

R-package for the analysis of Thermo Orbitrap Fusion Top-Down Proteomic Data.

https://github.com/sgibb/topdownr

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.6%) to scientific vocabulary

Keywords

mass-spectrometry proteomics r topdown

Keywords from Contributors

bioconductor-package ontology gene visualisation spatial-proteomics proteomics-data proteomexchange bioconductor metabolomics gene-expression
Last synced: 6 months ago · JSON representation

Repository

R-package for the analysis of Thermo Orbitrap Fusion Top-Down Proteomic Data.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 4
  • Forks: 0
  • Open Issues: 12
  • Releases: 0
Topics
mass-spectrometry proteomics r topdown
Created almost 10 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog Contributing License Support

README.md

topdownr

Project Status: Active - The project has reached a stable, usable state and is being actively developed. build status codecov.io license

years in bioc bioc downloads Release: build release Devel: build devel <!-- badges: end -->

Installation

r if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("topdownr")

If you want to install the development version from github (not recommended unless you know what you are doing):

r if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("sgibb/topdownr")

Documentation

To get started:

r ?"topdownr-package" vignette("data-generation", package="topdownr") vignette("analysis", package="topdownr")

Development documentation: https://sgibb.github.io/topdownr/

Questions

General questions should be asked on the Bioconductor support forum, using topdownr to tag the question. Feel also free to open a GitHub issue, in particular for bug reports.

Contribution

See CONTRIBUTING.md.

Support

See SUPPORT.md.

Owner

  • Name: Sebastian Gibb
  • Login: sgibb
  • Kind: user
  • Location: Greifswald, Germany
  • Company: University Medicine Greifswald

GitHub Events

Total
  • Issues event: 2
  • Delete event: 1
  • Push event: 3
  • Create event: 1
Last Year
  • Issues event: 2
  • Delete event: 1
  • Push event: 3
  • Create event: 1

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 603
  • Total Committers: 8
  • Avg Commits per committer: 75.375
  • Development Distribution Score (DDS): 0.055
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Sebastian Gibb m****l@s****e 570
Nitesh Turaga n****a@g****m 14
J Wokaty j****y@s****u 6
Hervé Pagès h****s@f****g 5
vobencha v****n@r****g 3
vobencha v****a@g****m 2
pavel-shliaha p****s@b****k 2
Kayla-Morrell k****l@r****g 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 bmb.sdu.dk: 1 fredhutch.org: 1 sph.cuny.edu: 1 sebastiangibb.de: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 84
  • Total pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 6
  • Total pull request authors: 0
  • Average comments per issue: 4.39
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • pavel-shliaha (49)
  • sgibb (28)
  • Me9atron (3)
  • malenasj (2)
  • mbabovic (1)
  • veitveit (1)
Pull Request Authors
Top Labels
Issue Labels
feature request (19) TODO (18) question (16) enhancement (9) bug (8) wontfix (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 13,694 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: topdownr

Investigation of Fragmentation Conditions in Top-Down Proteomics

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 13,694 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Forks count: 19.8%
Average: 22.1%
Stargazers count: 29.0%
Downloads: 61.7%
Maintainers (1)
mail@sebastiangibb.de
Last synced: 6 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
DESCRIPTION cran
  • BiocGenerics >= 0.20.0 depends
  • Biostrings >= 2.42.1 depends
  • ProtGenerics >= 1.10.0 depends
  • R >= 3.5 depends
  • S4Vectors >= 0.12.2 depends
  • methods * depends
  • Biobase * imports
  • MSnbase >= 2.3.10 imports
  • Matrix >= 1.4 imports
  • ggplot2 >= 2.2.1 imports
  • grDevices * imports
  • mzR >= 2.27.5 imports
  • stats * imports
  • tools * imports
  • utils * imports
  • BiocStyle * suggests
  • knitr * suggests
  • ranger * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • topdownrdata >= 0.2 suggests
  • xml2 * suggests