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| Format: | Recurso digital |
| Language: | English |
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2024
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| Online Access: | https://doi.org/10.5281/zenodo.11120878 |
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| _version_ | 1866902046432559104 |
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| author | Schork, Karin |
| author_facet | Schork, Karin |
| contents | <p>This R Code belongs to the doctoral thesis of Karin Schork "Improvement of protein quantification for proteins with shared peptides by using bipartite peptide-protein graphs". This repository provides code for using bipartite peptide-protein graphs to improve protein quantification in mass spectrometry-based bottom-up proteomics with a special focus on proteins without shared peptides.</p> <p>Folders beginning with DISS_ indicate R code used for generating graphs and tables for the dissertation.</p> <p>The installation of the bppg R package is required, which can be done using the following code:</p> <div> <pre><code>install.packages("devtools") devtools::install_git(url = "https://gitlab.ruhr-uni-bochum.de/mpc-bioinformatics/bppg.git")</code></pre> </div> <p>Further developments will be integrated to the bppg R package. The development version of this package can be found at github <a href="https://github.com/mpc-bioinformatics/bppg" target="_blank" rel="nofollow noreferrer noopener">https://github.com/mpc-bioinformatics/bppg</a> .</p> <p>------------------------------------------------------------------------------------------------------------</p> <p>Copyright Ruhr University Bochum, Medizinisches Proteom-Center 2024</p> <p>This software is released under a three-clause BSD license:</p> <p>Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:</p> <ul> <li> <p>Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</p> </li> <li> <p>Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</p> </li> <li> <p>Neither the name of any author or any participating institution may be used to endorse or promote products derived from this software without specific prior written permission.</p> </li> </ul> <p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_11120878 |
| institution | Zenodo |
| language | eng |
| publishDate | 2024 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Improvement of protein quantification for proteins with shared peptides by using bipartite peptide-protein graphs Schork, Karin <p>This R Code belongs to the doctoral thesis of Karin Schork "Improvement of protein quantification for proteins with shared peptides by using bipartite peptide-protein graphs". This repository provides code for using bipartite peptide-protein graphs to improve protein quantification in mass spectrometry-based bottom-up proteomics with a special focus on proteins without shared peptides.</p> <p>Folders beginning with DISS_ indicate R code used for generating graphs and tables for the dissertation.</p> <p>The installation of the bppg R package is required, which can be done using the following code:</p> <div> <pre><code>install.packages("devtools") devtools::install_git(url = "https://gitlab.ruhr-uni-bochum.de/mpc-bioinformatics/bppg.git")</code></pre> </div> <p>Further developments will be integrated to the bppg R package. The development version of this package can be found at github <a href="https://github.com/mpc-bioinformatics/bppg" target="_blank" rel="nofollow noreferrer noopener">https://github.com/mpc-bioinformatics/bppg</a> .</p> <p>------------------------------------------------------------------------------------------------------------</p> <p>Copyright Ruhr University Bochum, Medizinisches Proteom-Center 2024</p> <p>This software is released under a three-clause BSD license:</p> <p>Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:</p> <ul> <li> <p>Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</p> </li> <li> <p>Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</p> </li> <li> <p>Neither the name of any author or any participating institution may be used to endorse or promote products derived from this software without specific prior written permission.</p> </li> </ul> <p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</p> |
| title | Improvement of protein quantification for proteins with shared peptides by using bipartite peptide-protein graphs |
| url | https://doi.org/10.5281/zenodo.11120878 |