Commit 6908bc9d authored by TomKellyGenetics's avatar TomKellyGenetics
Browse files

update citation to biorxiv preprint:

parent d239d32a

README.Rmd

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@@ -182,21 +182,39 @@ focus on the results. 


### Citation <span id="Citation"><span>



A submission to a journal and biorXiv is in progress. Please cite this

when it becomes available. In the meantime, the package can be cited

A submission to a journal and biorXiv is in progress. Please cite these when

they are available. Currently, the package can be cited

as follows:



Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: single-cell processing across technologies.

package version 1.0.2. https://github.com/TomKellyGenetics/universc

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        URL = {https://github.com/minoda-lab/universc},

}



```



```

@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    url = {https://github.com/TomKellyGenetics/universc},

    url = {https://github.com/minoda-lab/universc},

  }

```

README.html

+20 −6
Original line number Diff line number Diff line
@@ -76,14 +76,28 @@ 
<p>This tool will be released open-source (see <a href="#licensing">legal stuff</a> below). We welcome any feedback on it and any contributions to improve it. Hopefully it will save people time by making it easier to compare technologies.</p>

<p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>

<h3 id="citation">Citation <span id="Citation"><span></h3>

<p>A submission to a journal and biorXiv is in progress. Please cite this when it becomes available. In the meantime, the package can be cited as follows:</p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: single-cell processing across technologies. package version 1.0.2. https://github.com/TomKellyGenetics/universc</p>

<p>A submission to a journal and biorXiv is in progress. Please cite these when they are available. Currently, the package can be cited as follows:</p>

<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.0.2. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>

<pre><code>@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        URL = {https://github.com/minoda-lab/universc},

}

</code></pre>

<pre><code>@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    url = {https://github.com/TomKellyGenetics/universc},

    url = {https://github.com/minoda-lab/universc},

  }</code></pre>

<h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>

<h4 id="reporting-issues">Reporting issues</h4>

README.md

+26 −8
Original line number Diff line number Diff line
@@ -182,21 +182,39 @@ focus on the results. 


### Citation <span id="Citation"><span>



A submission to a journal and biorXiv is in progress. Please cite this

when it becomes available. In the meantime, the package can be cited

A submission to a journal and biorXiv is in progress. Please cite these when

they are available. Currently, the package can be cited

as follows:



Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: single-cell processing across technologies.

package version 1.0.2. https://github.com/TomKellyGenetics/universc

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        URL = {https://github.com/minoda-lab/universc},

}



```



```

@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    url = {https://github.com/TomKellyGenetics/universc},

    url = {https://github.com/minoda-lab/universc},

  }

```

inst/CITATION

+28 −10
Original line number Diff line number Diff line 
### Citation <span id="Citation"><span>



A submission to a journal and biorXiv is in progress. Please cite this

when it becomes available. In the meantime, the package can be cited

A submission to a journal and biorXiv is in progress. Please cite these when

they are available. Currently, the package can be cited

as follows:



Kelly, S.T., Battenberg, K., Hayashi, K., and Minoda, A. (2020)

launch_universc.sh : single-cell processing across technologies.

package version 1.0.0. https://github.com/TomKellyGenetics/universc

Kelly, S.T., Battenberg, Hetherington, N.A., K., Hayashi, K., and Minoda, A. (2021)

UniverSC: a flexible cross-platform single-cell data processing pipeline.

bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)

package version 1.0.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)



```

@article {Kelly2021.01.19.427209,

        author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},

        title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},

        elocation-id = {2021.01.19.427209},

        year = {2021},

        doi = {10.1101/2021.01.19.427209},

        publisher = {Cold Spring Harbor Laboratory},

        abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},

        eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},

        journal = {{bioRxiv}},

        note = {package version 1.0.2},

        URL = {https://github.com/minoda-lab/universc},

}



```



```

@Manual{,

    title = {{launch_universc.sh}: single-cell processing across technologies},

    author = {S. Thomas Kelly, Kai Battenbery, Makoto Hayashi, and Aki Minoda},

    year = {2020},

    note = {package version 1.0.0},

    url = {https://github.com/TomKellyGenetics/universc},

    title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},

    author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},

    year = {2021},

    note = {package version 1.0.2},

    url = {https://github.com/minoda-lab/universc},

  }

```

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