# HG changeset patch
# User mingchen0919
# Date 1502207142 14400
# Node ID 15a5fb1a2ac8dafd151ed479dcba50d008202094
# Parent  a0d37b034e45c7a34be947d6244a9fbf51e287d7
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty

diff -r a0d37b034e45 -r 15a5fb1a2ac8 DESeq.xml
--- a/DESeq.xml	Tue Aug 08 10:56:49 2017 -0400
+++ b/DESeq.xml	Tue Aug 08 11:45:42 2017 -0400
@@ -77,4 +77,54 @@
         <data name="DESeq" format="html" label="DESeq Analysis" />
         <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
     </outputs>
+    <citations>
+        <citation>
+            @article{love2014moderated,
+            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
+            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
+            journal={Genome biology},
+            volume={15},
+            number={12},
+            pages={550},
+            year={2014},
+            publisher={BioMed Central}
+            }
+        </citation>
+        <citation type="bibtex">
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+        <citation>
+            @misc{pheatmap2015,
+            title = {pheatmap: Pretty Heatmaps},
+            author = {Raivo Kolde},
+            year = {2015},
+            note = {R package version 1.0.8},
+            url = {https://CRAN.R-project.org/package=pheatmap},
+            }
+        </citation>
+        <citation>
+            @misc{dt2016,
+            title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
+            author = {Yihui Xie},
+            year = {2016},
+            note = {R package version 0.2},
+            url = {https://CRAN.R-project.org/package=DT},
+            }
+        </citation>
+    </citations>
 </tool>
\ No newline at end of file
diff -r a0d37b034e45 -r 15a5fb1a2ac8 DESeq_results.xml
--- a/DESeq_results.xml	Tue Aug 08 10:56:49 2017 -0400
+++ b/DESeq_results.xml	Tue Aug 08 11:45:42 2017 -0400
@@ -85,4 +85,54 @@
     <outputs>
         <data name="deseq_results" format="html" label="DESeq Results" />
     </outputs>
+    <citations>
+        <citation>
+            @article{love2014moderated,
+            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
+            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
+            journal={Genome biology},
+            volume={15},
+            number={12},
+            pages={550},
+            year={2014},
+            publisher={BioMed Central}
+            }
+        </citation>
+        <citation type="bibtex">
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+        <citation>
+            @misc{pheatmap2015,
+            title = {pheatmap: Pretty Heatmaps},
+            author = {Raivo Kolde},
+            year = {2015},
+            note = {R package version 1.0.8},
+            url = {https://CRAN.R-project.org/package=pheatmap},
+            }
+        </citation>
+        <citation>
+            @misc{dt2016,
+            title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
+            author = {Yihui Xie},
+            year = {2016},
+            note = {R package version 0.2},
+            url = {https://CRAN.R-project.org/package=DT},
+            }
+        </citation>
+    </citations>
 </tool>
\ No newline at end of file
diff -r a0d37b034e45 -r 15a5fb1a2ac8 DESeq_visualization.xml
--- a/DESeq_visualization.xml	Tue Aug 08 10:56:49 2017 -0400
+++ b/DESeq_visualization.xml	Tue Aug 08 11:45:42 2017 -0400
@@ -91,4 +91,54 @@
     <outputs>
         <data name="deseq_visualization" format="html" label="DESeq Visualization" />
     </outputs>
+    <citations>
+        <citation>
+            @article{love2014moderated,
+            title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
+            author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
+            journal={Genome biology},
+            volume={15},
+            number={12},
+            pages={550},
+            year={2014},
+            publisher={BioMed Central}
+            }
+        </citation>
+        <citation type="bibtex">
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        </citation>
+        <citation type="bibtex">
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        </citation>
+        <citation>
+            @misc{pheatmap2015,
+            title = {pheatmap: Pretty Heatmaps},
+            author = {Raivo Kolde},
+            year = {2015},
+            note = {R package version 1.0.8},
+            url = {https://CRAN.R-project.org/package=pheatmap},
+            }
+        </citation>
+        <citation>
+            @misc{dt2016,
+            title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
+            author = {Yihui Xie},
+            year = {2016},
+            note = {R package version 0.2},
+            url = {https://CRAN.R-project.org/package=DT},
+            }
+        </citation>
+    </citations>
 </tool>
\ No newline at end of file