https://github.com/compomics/search-all-assess-subset
An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.
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An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.
Basic Info
- Host: GitHub
- Owner: CompOmics
- Language: HTML
- Default Branch: master
- Homepage: https://compomics.github.io/search-all-assess-subset/
- Size: 4.62 MB
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- Stars: 1
- Watchers: 3
- Forks: 2
- Open Issues: 2
- Releases: 0
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Created over 9 years ago
· Last pushed over 8 years ago
https://github.com/CompOmics/search-all-assess-subset/blob/master/
# search-all-assess-subset An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics. The search-all-assess-subset FDR procedure has been published in [Sticker et al. Nature Methods 14, 643644 (2017) doi:10.1038/nmeth.4338](https://doi.org/10.1038/nmeth.4338) >Mass spectrometrists should search for all peptides, but assess only the ones they care about
>(Adriaan Sticker, Lennart Martens, Lieven Clement) Please include this reference if you use search-all-assess-subset FDR procedure as part of a publication. A user-friendly GUI version of saas is hosted [here](http://iomics.ugent.be/saas/). More information on the FDR estimation procedure for subsets and the usage of the SAAS package can be found in the [vignette](https://compomics.github.io/search-all-assess-subset/articles/saas.html) ## Installation You first need to install the [devtools](https://cran.r-project.org/package=devtools) package. ```r install.packages("devtools") ``` Then install saas using the `install_github` function in the [devtools](https://cran.r-project.org/package=devtools) package. ```r library(devtools) install_github("compomics/search-all-assess-subset") ``` ## Running the saas GUI When saas is installed, you can easily launch the GUI from R. By default, you can see the GUI by visiting [http://127.0.0.1:3320](http://127.0.0.1:3320) ```r library(saas) saas_gui() ``` Or if you want to run saas immediately from the terminal. ```r R -e "library(saas);saas_gui()" ```
Owner
- Name: Computational Omics and Systems Biology Group
- Login: CompOmics
- Kind: organization
- Email: compomics.list@gmail.com
- Website: https://www.compomics.com/
- Twitter: CompOmics
- Repositories: 93
- Profile: https://github.com/CompOmics
The CompOmics group, headed by Prof. Dr. Lennart Martens, specializes in the management, analysis and integration of high-throughput Omics data.