Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.1%) to scientific vocabulary
Keywords
mass-spectrometry
peptide-spectrum-matches
proteomics
rstats
Keywords from Contributors
bioconductor
metabolomics
bioconductor-package
hdf5
rhdf5
Last synced: 6 months ago
·
JSON representation
Repository
Peptide Spectrum Matching
Basic Info
- Host: GitHub
- Owner: rformassspectrometry
- Language: R
- Default Branch: main
- Homepage: https://rformassspectrometry.github.io/PSMatch
- Size: 18.9 MB
Statistics
- Stars: 4
- Watchers: 3
- Forks: 2
- Open Issues: 3
- Releases: 0
Topics
mass-spectrometry
peptide-spectrum-matches
proteomics
rstats
Created over 5 years ago
· Last pushed 7 months ago
Metadata Files
Readme
Changelog
README.md
Handling peptide-spectrum matches
PSMatch is a simple package to load, process and analyse PSMs
(Peptide-Spectrum Matches). The following references are a good way to
get started with the package:
- The package manual
package
for a general overview of the main concepts tackled by the
PSMatchpackage. - The Working with PSM
data
vignette to learn about the
PSMto read and filter peptide-spectrum matches. - The Understanding protein groups with adjacency matrices vignette to learn about adjaceny matrices and connected components to explore and manage protein groups.
- The MS2 fragment ions vignette to calculate and visualise MS2 fragment ions.
Installation instructions
To install the package from Bioconductor, make sure you have the
BiocManager package, available from CRAN, and then run
r
BiocManager::install("PSMatch")
Credit
Code in this package is partly composed of functions ported from
MSnbase with the goal to (1)
make them more general and (2) integrate them with the R for Mass
Spectrometry
infrastructure.
Owner
- Name: RforMassSpectrometry
- Login: rformassspectrometry
- Kind: organization
- Email: maintainer@rformassspectrometry.org
- Website: https://www.rformassspectrometry.org/
- Repositories: 33
- Profile: https://github.com/rformassspectrometry
R packages for mass spectrometry
GitHub Events
Total
- Issues event: 8
- Watch event: 1
- Issue comment event: 43
- Push event: 54
- Pull request event: 21
- Pull request review event: 64
- Pull request review comment event: 74
- Fork event: 1
- Create event: 2
Last Year
- Issues event: 8
- Watch event: 1
- Issue comment event: 43
- Push event: 54
- Pull request event: 21
- Pull request review event: 64
- Pull request review comment event: 74
- Fork event: 1
- Create event: 2
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| lgatto | l****o@g****m | 258 |
| Guitou1 | p****f@g****m | 113 |
| Guillaume | g****e@d****e | 14 |
| J Wokaty | j****y@s****u | 10 |
| Sebastian Gibb | m****l@s****e | 4 |
| Nitesh Turaga | n****a@g****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 20
- Total pull requests: 22
- Average time to close issues: 5 months
- Average time to close pull requests: 14 days
- Total issue authors: 5
- Total pull request authors: 3
- Average comments per issue: 0.95
- Average comments per pull request: 2.09
- Merged pull requests: 15
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 21
- Average time to close issues: 20 days
- Average time to close pull requests: 15 days
- Issue authors: 2
- Pull request authors: 2
- Average comments per issue: 0.67
- Average comments per pull request: 2.19
- Merged pull requests: 14
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lgatto (12)
- guideflandre (4)
- HijaziHassan (2)
- BaylorSci (1)
- sgibb (1)
Pull Request Authors
- guideflandre (17)
- sgibb (4)
- lgatto (1)
Top Labels
Issue Labels
question (1)
Pull Request Labels
enhancement (2)
Dependencies
DESCRIPTION
cran
- S4Vectors * depends
- BiocGenerics * imports
- BiocParallel * imports
- Matrix * imports
- MsCoreUtils * imports
- ProtGenerics >= 1.27.1 imports
- QFeatures * imports
- igraph * imports
- methods * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- Spectra * suggests
- SummarizedExperiment * suggests
- factoextra * suggests
- knitr * suggests
- msdata * suggests
- mzID * suggests
- mzR * suggests
- rmarkdown * suggests
- rpx * suggests
- testthat * suggests
.github/workflows/check-bioc.yml
actions
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite