MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
Science Score: 59.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
5 of 39 committers (12.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.1%) to scientific vocabulary
Keywords
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Repository
Base Classes and Functions for Mass Spectrometry and Proteomics
Basic Info
- Host: GitHub
- Owner: lgatto
- Language: R
- Default Branch: master
- Homepage: http://lgatto.github.io/MSnbase/
- Size: 112 MB
Statistics
- Stars: 134
- Watchers: 13
- Forks: 47
- Open Issues: 10
- Releases: 0
Topics
Metadata Files
README.md
The MSnbase package
MSnbase is an R/Bioconductor package that provides infrastructure for plotting, manipulation and processing mass spectrometry and proteomics data. The project was started by Laurent Gatto in October 2010 (Mon Oct 4 23:35:23 2010, according to the git log) and has, since then, benefited from various contributions, in particular Sebastian Gibb and Johannes Rainer.
The official package page is the Bioconductor landing page (release or devel versions). The github page page is for active development, issue tracking and forking/pulling purposes.
To get an overview of the package, see the MSnbase-demo vignette. More vignettes are available in the Articles tab.
The R for Mass Spectrometry initiative
The aim of the R for Mass Spectrometry initiative is to provide efficient, thoroughly documented, tested and flexible R software for the analysis and interpretation of high throughput mass spectrometry assays, including proteomics and metabolomics experiments. The project formalises the longtime collaborative development efforts of its core members under the R for Mass Spectrometry organisation to facilitate dissemination and accessibility of their work.
If you are using MSnbase, consider switching to the R for Mass Spectrometry packages, in particular, Spectra for raw data, PSMatch for identification data, and QFeatures for quantitative data. See https://RforMassSpectrometry.org for details.
Installation
To install the package:
r
install.packages("BiocManager")
BiocManager::install("MSnbase")
If you need the github version (not recommended unless you know what you are doing), use
r
BiocManager::install("lgatto/MSnbase")
Questions
General questions should be asked on
the Bioconductor support forum,
using MSnbase to tag the question. Feel also free to open a
GitHub issue, in
particular for bug reports.
Citation
To cite the MSnbase package in publications, please use:
Gatto L, Lilley KS.
MSnbase- an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics. 2012 Jan 15;28(2):288-9. doi:10.1093/bioinformatics/btr645. PubMed PMID:22113085.
MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data. Laurent Gatto, Sebastian Gibb, Johannes Rainer. bioRxiv 2020.04.29.067868; doi: https://doi.org/10.1101/2020.04.29.067868
Contributing
Contributions to the package are more than welcome. If you want to
contribute to this package, you should follow the same conventions as
the rest of the functions. Please do get in touch (preferable opening
a github issue) to
discuss any suggestions. The
MSnbase development vignette gives
some background on the class infrastructure.
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
Owner
- Name: Laurent Gatto
- Login: lgatto
- Kind: user
- Location: Belgium
- Company: de Duve Institute, UCLouvain
- Website: https://fosstodon.org/@lgatto
- Repositories: 98
- Profile: https://github.com/lgatto
Open science, reproducible research, bioinformatics, computational biology, proteomics, more omics, emacs, a lot of R, running and parenting.
GitHub Events
Total
- Issues event: 7
- Watch event: 8
- Issue comment event: 11
- Push event: 20
- Pull request review event: 1
- Pull request event: 3
- Fork event: 2
- Create event: 1
Last Year
- Issues event: 7
- Watch event: 8
- Issue comment event: 11
- Push event: 20
- Pull request review event: 1
- Pull request event: 3
- Fork event: 2
- Create event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Laurent | l****0@c****k | 1,182 |
| Laurent | l****o@g****m | 581 |
| l.gatto | l****o@b****8 | 450 |
| Laurent Gatto | l****o@d****e | 418 |
| jotsetung | j****r@g****m | 346 |
| Sebastian Gibb | m****l@s****e | 304 |
| d.tenenbaum | d****m@b****8 | 46 |
| Dan Tenenbaum | d****a@f****g | 28 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 10 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 9 |
| Steffen Neumann | s****n@i****e | 9 |
| Herve Pages | h****s@f****g | 6 |
| Flora Liu | f****u@g****m | 5 |
| Hervé Pagès | h****s@f****g | 4 |
| vladpetyuk | p****k@g****m | 4 |
| const-ae | a****5@g****m | 4 |
| adder | a****r@g****m | 4 |
| Arne Hindrik Smits | a****s@e****e | 4 |
| Henk van den Toorn | v****n@h****m | 3 |
| Rico Derks | r****s@l****l | 3 |
| Johannes Rainer | jo@m****l | 3 |
| vobencha | v****n@r****g | 2 |
| s.arora | s****a@b****8 | 2 |
| Martifis | f****m@r****e | 2 |
| vobencha | v****a@g****m | 2 |
| Pascal | p****2@g****m | 2 |
| Jan Stanstrup | s****p@g****m | 2 |
| samWieczorek | s****k@c****r | 1 |
| lshep | s****l@g****m | 1 |
| and 9 more... | ||
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 167
- Total pull requests: 36
- Average time to close issues: over 1 year
- Average time to close pull requests: 7 days
- Total issue authors: 59
- Total pull request authors: 8
- Average comments per issue: 5.25
- Average comments per pull request: 2.75
- Merged pull requests: 36
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 2
- Average time to close issues: about 9 hours
- Average time to close pull requests: 24 days
- Issue authors: 5
- Pull request authors: 2
- Average comments per issue: 2.6
- Average comments per pull request: 1.5
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- lgatto (16)
- stanstrup (4)
- ibphuangchen (3)
- cyan20200410 (3)
- MuyaoXi9271 (2)
- pavel-shliaha (2)
- ricoderks (2)
- jamesrgraham (2)
- Lasseeli (2)
- sgibb (2)
- plbaldoni (2)
- cbroeckl (2)
- jmorim (2)
- Mahmoudhallal (1)
- YANGJJ93research (1)
Pull Request Authors
- jorainer (16)
- sgibb (2)
- vdtoorn (1)
- Pascallio (1)
- MiguelCos (1)
- Adafede (1)
- lmsimp (1)
- hpages (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 494,682 total
- Total dependent packages: 30
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: MSnbase
Base Functions and Classes for Mass Spectrometry and Proteomics
- Homepage: https://lgatto.github.io/MSnbase
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/MSnbase/inst/doc/MSnbase.pdf
- License: Artistic-2.0
-
Latest release: 2.34.1
published 9 months ago
Rankings
Maintainers (1)
Dependencies
- Biobase >= 2.15.2 depends
- BiocGenerics >= 0.7.1 depends
- ProtGenerics >= 1.27.2 depends
- R >= 3.5 depends
- S4Vectors * depends
- methods * depends
- mzR >= 2.29.3 depends
- BiocParallel * imports
- IRanges >= 2.13.28 imports
- MALDIquant >= 1.16 imports
- MASS * imports
- MsCoreUtils * imports
- Rcpp * imports
- XML * imports
- affy * imports
- digest * imports
- ggplot2 * imports
- grid * imports
- impute * imports
- lattice * imports
- mzID >= 1.5.2 imports
- pcaMethods * imports
- plyr * imports
- scales * imports
- stats4 * imports
- vsn * imports
- AnnotationHub * suggests
- BiocStyle >= 2.5.19 suggests
- Rdisop * suggests
- SummarizedExperiment * suggests
- gplots * suggests
- gridExtra * suggests
- imputeLCMD * suggests
- knitr >= 1.1.0 suggests
- magrittr * suggests
- microbenchmark * suggests
- msdata >= 0.19.3 suggests
- norm * suggests
- pRoloc * suggests
- pRolocdata >= 1.7.1 suggests
- pryr * suggests
- rgl * suggests
- rmarkdown * suggests
- rols * suggests
- roxygen2 * suggests
- rpx * suggests
- shiny * suggests
- testthat * suggests
- zoo * suggests
- actions/cache v1 composite
- actions/checkout v2 composite
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