isobar
isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data
Science Score: 20.0%
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
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: scholar.google -
✓Committers with academic emails
4 of 20 committers (20.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.3%) to scientific vocabulary
Keywords from Contributors
Repository
isobar - R library for the Analysis and quantitation of isobarically tagged MSMS proteomics data
Basic Info
- Host: GitHub
- Owner: fbreitwieser
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/release/bioc/html/isobar.html
- Size: 13.5 MB
Statistics
- Stars: 10
- Watchers: 3
- Forks: 8
- Open Issues: 5
- Releases: 0
Metadata Files
README.md
isobar - R package for iTRAQ and TMT proteomics data
isobar provides methods for preprocessing, normalization, and
report generation for the analysis of proteomics data generated by Mass
spectrometers using isobaric peptide tags, such as iTRAQ and TMT.
PDF and Excel reports can automatically be generated based on a configuration file.
Include modules for validating and integrating data focussing on
post-translational protein modifications (isobar-PTM).
Installation
The official Bioconductor version can be found at http://bioconductor.org/packages/release/bioc/html/isobar.html
To install isobar from Bioconductor, call
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("isobar")
To install the development version of isobar, the easiest way is using the devtools package:
## install.package("devtools") # if you do not have the devtools package
devtools::install_github("fbreitwieser/isobar")
The following packages are suggested for some uses in isobar, and maybe should be installed as well: MSnbase, OrgMassSpecR, biomaRt, Hmisc, gplots and limma.
References
- Florian P. Breitwieser, André Müller, Loïc Dayon, Thomas Köcher, Alexandre Hainard, Peter Pichler, Ursula Schmidt-Erfurth, Giulio Superti-Furga, Jean-Charles Sanchez, Karl Mechtler, Keiryn L. Bennett, and Jacques Colinge (June 2011). “General statistical modeling of data from protein relative expression isobaric tags.” In: J Proteome Res 10.6, pp. 2758–2766
- Florian P. Breitwieser and Jacques Colinge (Sept. 2013). “Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins.” eng. In: J Proteomics 90, pp. 77–84
For publications citing isobar please see Google scholar for isobar and isobar PTM.
Many thanks to Alexey Stukalov, Xavier Robin and Florent Gluck who contributed to the development of the package.
Owner
- Name: Florian Breitwieser
- Login: fbreitwieser
- Kind: user
- Website: http://www.ccb.jhu.edu/people/florian/
- Repositories: 79
- Profile: https://github.com/fbreitwieser
Babboon By: Henry Henderson | License: Creative Commons Attribution (CC BY 4.0)
GitHub Events
Total
Last Year
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Florian Breitwieser | f****r@c****t | 580 |
| f.breitwieser | f****r@b****8 | 190 |
| d.tenenbaum | d****m@b****8 | 25 |
| Florian Breitwieser | f****w@g****m | 17 |
| Alexey Stukalov | a****v@g****m | 16 |
| fbreitw1@jhu.edu | F****r | 9 |
| Johannes Griss | j****s | 3 |
| Alexey Stukalov | a****v@c****t | 3 |
| Bioconductor Git-SVN Bridge | b****c@b****g | 3 |
| Johannes Griss | j****8@y****m | 3 |
| Florent Gluck | f****k@n****6 | 2 |
| Alexey Stukalov | A****v@c****t | 1 |
| Florent Gluck | f****k@S****) | 1 |
| Jacques Colinge | j****e@c****t | 1 |
| ahainard | a****d@r****m | 1 |
| hpages@fhcrc.org | h****s@f****g@b****8 | 1 |
| m.carlson | m****n@b****8 | 1 |
| mtmorgan@fhcrc.org | m****n@f****g@b****8 | 1 |
| s.arora | s****a@b****8 | 1 |
| unknown | k****n@c****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 5
- Total pull requests: 15
- Average time to close issues: 5 months
- Average time to close pull requests: 10 days
- Total issue authors: 5
- Total pull request authors: 4
- Average comments per issue: 0.6
- Average comments per pull request: 0.6
- Merged pull requests: 14
- 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
Top Authors
Issue Authors
- jgriss (1)
- pvannierop (1)
- veitveit (1)
- mdkasoji (1)
- simpar1471 (1)
Pull Request Authors
- alyst (11)
- jgriss (2)
- fbreitwieser (1)
- ahainard (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 41,274 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: isobar
Analysis and quantitation of isobarically tagged MSMS proteomics data
- Homepage: https://github.com/fbreitwieser/isobar
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/isobar/inst/doc/isobar.pdf
- License: LGPL-2
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Latest release: 1.54.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- Biobase * depends
- R >= 2.10.0 depends
- methods * depends
- stats * depends
- distr * imports
- plyr * imports
- DBI * suggests
- Hmisc * suggests
- MASS * suggests
- MSnbase * suggests
- OrgMassSpecR * suggests
- RColorBrewer * suggests
- RJSONIO * suggests
- XML * suggests
- biomaRt * suggests
- boot * suggests
- distr * suggests
- ggplot2 * suggests
- gplots * suggests
- gridExtra * suggests
- limma * suggests