| Previous changeset 69:19d704e24977 (2020-04-23) Next changeset 71:64bb96d3c121 (2020-06-03) |
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Commit message:
update links and pubblications. |
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modified:
Marea/local/HMRcoreMap.svg Marea/local/HMRcore_genes.p Marea/local/HMRcore_rules.p Marea/local/Recon_genes.p Marea/local/Recon_rules.p Marea/local/desktop.ini Marea/marea.py Marea/marea.xml Marea/marea_cluster.py Marea/marea_cluster.xml Marea/marea_macros.xml Marea/ras_generator.py Marea/ras_generator.xml |
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| diff -r 19d704e24977 -r c22ba0547370 Marea/marea.xml --- a/Marea/marea.xml Thu Apr 23 17:17:41 2020 -0400 +++ b/Marea/marea.xml Wed Jun 03 10:19:48 2020 -0400 |
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| @@ -277,13 +277,18 @@ **TIP**: If your dataset is not split into classes, use `MaREA cluster analysis`_. +.. class:: infomark + +**TIP**: This tool using the RAS scores computed by `Ras tool`_. + @REFERENCE@ -.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 -.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj -.. _MaREA cluster analysis: http://link del tool di cluster.org +.. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76 +.. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6 +.. _MaREA cluster analysis: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA_cluester%2F1.1.2&version=1.1.2&__identifer=lxbyzn2me9 ]]> </help> -<expand macro="citations" />undefined</tool> +<expand macro="citations" /> +</tool> |
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| diff -r 19d704e24977 -r c22ba0547370 Marea/marea_cluster.xml --- a/Marea/marea_cluster.xml Thu Apr 23 17:17:41 2020 -0400 +++ b/Marea/marea_cluster.xml Wed Jun 03 10:19:48 2020 -0400 |
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| @@ -132,8 +132,7 @@ .. class:: infomark -**TIP**: This tool has been conceived to cluster gene expression data, by using the RAS scores computed by the tool -`MaREA`_ as feature +**TIP**: This tool has been conceived to cluster gene expression data, by using the RAS scores computed by `Ras tool`_. .. class:: infomark @@ -143,8 +142,8 @@ @REFERENCE@ -.. _MaREA: https://www.biorxiv.org/content/early/2018/01/16/248724 -.. _Convert delimiters to TAB: https://usegalaxy.org/?tool_id=Convert+characters1&version=1.0.0&__identifer=6t22teyofhj +.. _Ras tool: http://bimib.disco.unimib.it:5555/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbimib%2Fmarea%2FMaREA+RAS+Generator%2F1.0.6&version=1.0.6&__identifer=auulv6gbp76 +.. _Convert delimiters to TAB: http://bimib.disco.unimib.it:5555/?tool_id=Convert+characters1&version=1.0.0&__identifer=76g7trea4j6 ]]> |
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| diff -r 19d704e24977 -r c22ba0547370 Marea/marea_macros.xml --- a/Marea/marea_macros.xml Thu Apr 23 17:17:41 2020 -0400 +++ b/Marea/marea_macros.xml Wed Jun 03 10:19:48 2020 -0400 |
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| @@ -68,7 +68,7 @@ This tool is developed by the `BIMIB`_ at the `Department of Informatics, Systems and Communications`_ of `University of Milan - Bicocca`_. -.. _BIMIB: http://sito di bio.org +.. _BIMIB: https://bimib.disco.unimib.it/index.php/Home .. _Department of Informatics, Systems and Communications: http://www.disco.unimib.it/go/Home/English .. _University of Milan - Bicocca: https://www.unimib.it/ @@ -77,14 +77,28 @@ <xml name="citations"> <citations> <!--esempio di citazione--> <citation type="bibtex"> -@online{lh32017, - author = {Alex Graudenzi, Davide Maspero, Cluadio Isella, Marzia Di Filippo, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani}, - year = {2018}, - title = {MaREA: Metabolic feature extraction, enrichment and visualization of RNAseq}, - publisher = {bioRxiv}, - journal = {bioRxiv}, - url = {https://www.biorxiv.org/content/early/2018/01/16/248724}, -} + @article{graudenzi2018integration, + title={Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power}, + author={Graudenzi, Alex and Maspero, Davide and Di Filippo, Marzia and Gnugnoli, Marco and Isella, Claudio and Mauri, Giancarlo and Medico, Enzo and Antoniotti, Marco and Damiani, Chiara}, + journal={Journal of biomedical informatics}, + volume={87}, + pages={37--49}, + year={2018}, + publisher={Elsevier}, + url = {https://doi-org.proxy.unimib.it/10.1016/j.jbi.2018.09.010}, + } + </citation> + <citation type="bibtex"> + @article{damiani2020marea4galaxy, + title={MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy}, + author={Damiani, Chiara and Rovida, Lorenzo and Maspero, Davide and Sala, Irene and Rosato, Luca and Di Filippo, Marzia and Pescini, Dario and Graudenzi, Alex and Antoniotti, Marco and Mauri, Giancarlo}, + journal={Computational and Structural Biotechnology Journal}, + volume={18}, + pages={993}, + year={2020}, + publisher={Research Network of Computational and Structural Biotechnology}, + url = {https://dx-doi-org.proxy.unimib.it/10.1016%2Fj.csbj.2020.04.008}, + } </citation> </citations> </xml> |
