https://github.com/uclouvain-cbio/sager
Analyse sage results in R
https://github.com/uclouvain-cbio/sager
bioconductor mass-spectrometry proteomics
Last synced: 3 months ago
JSON representation
Analyse sage results in R
- Host: GitHub
- URL: https://github.com/uclouvain-cbio/sager
- Owner: UCLouvain-CBIO
- Created: 2023-04-01T10:54:55.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-07-12T10:43:33.000Z (6 months ago)
- Last Synced: 2025-07-12T12:29:33.132Z (6 months ago)
- Topics: bioconductor, mass-spectrometry, proteomics
- Language: R
- Homepage: https://uclouvain-cbio.github.io/sager/
- Size: 1.08 MB
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
Awesome Lists containing this project
README
## `sager`: Analysing sage results with R
The `sager` package can be used to import results produced by the
[sage](https://lazear.github.io/sage/) search engine into R. Sage
produces tab-separated output files for identification and
quantitation results. In `sager`, we import these result files into
establised Bioconductor classes:
- Identification results are parsed and imported as
[PSM](https://rformassspectrometry.github.io/PSMatch/articles/PSM.html)
objects with
[sagePSM()](https://uclouvain-cbio.github.io/sager/reference/sagePSM.html).
- Quantitation (and identification) results are parsed, merged and
imported as
[QFeatures](https://rformassspectrometry.github.io/QFeatures/articles/QFeatures.html)
objects with
[sageQFeatures()](https://uclouvain-cbio.github.io/sager/reference/sageQFeatures.html).
These functions are described and demonstrated in their respective
manual pages using data generated from Yu *et al.* [Benchmarking the
Orbitrap Tribrid Eclipse for Next Generation Multiplexed
Proteomics](https://doi.org/10.1021/acs.analchem.9b05685), downloaded
from ProteomeXchange project
[PXD016766](https://www.ebi.ac.uk/pride/archive/projects/PXD016766). See
[sagerData()](https://uclouvain-cbio.github.io/sager/reference/sagerData.html)
for details.
If you want to install and try the package out:
```
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("UCLouvain-CBIO/sager")
```
If you run into issues of have questions, please open [an
issue](https://github.com/UCLouvain-CBIO/sager/issues).