# DIAlignR DIAlignR is an R package for retention time alignment of targeted mass spectrometric data, including DIA and SWATH-MS data. This tool works with MS2 chromatograms directly and uses dynamic programming for alignment of raw chromatographic traces. DIAlignR uses a hybrid approach of global (feature-based) and local (raw data-based) alignment to establish correspondence between peaks. [](https://travis-ci.org/shubham1637/DIAlignR) # Documentation For documentation please see [our vignette](https://htmlpreview.github.io/?https://github.com/shubham1637/DIAlignR/master/vignettes/DIAlignR-vignette.html). # Developing C++ code ``` cd DIAlignR mkdir build && cd build cmake -B. -H.. make clean && make && make test make runTest3 cd .. ``` Documenting C++ code ``` sudo apt install doxygen doxygen-gui sudo apt install graphviz cd DIAlignR cd src doxygen doc/Doxyfile ``` # Citation If you use the provided algorithms or the package, please cite our paper: Gupta S, Ahadi S, Zhou W, Röst H. "DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics." Mol Cell Proteomics. 2019 Apr;18(4):806-817. doi: https://doi.org/10.1074/mcp.TIR118.001132 Epub 2019 Jan 31. CNPN 2018 Poster doi: https://doi.org/10.6084/m9.figshare.6200837.v1 HUPO 2018 Poster doi: https://doi.org/10.6084/m9.figshare.7121696.v2