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What is Gitools ?
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Gitools is a framework for analysis and visualization of genomic data.
 Gitools allows importation of data directly from Biomart compatible databases
 and IntOGen facilitating the exploration and mining of large amount of
 oncogenomics data and allows performing several types of analyses, such
 as enrichment analyses, correlations, finding driver alterations and others.
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The main workflow is summarized in figure 
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reference "fig:The-main-workflow"

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.
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The main workflow summarized: The first step involves preparing the data
 to work with by editing files manually using Excel or any other well known
 program or alternativelly importing the data from any of the Gitools available
 data importers as Biomart or IntOGen.
 The second step consist in analyzing the data.
 There are different methods implemented as enrichment analysis, Z-weight
 combinations, correlations and oncogenomics driver alterations.
 The third step is to explore the data and the results using the implemented
 browsers where the heatmap allows to explore different results (for example
 for genes in rows) over different conditions (in columns).
 In th last step you can export the data, the results and the generated
 figures in different ways (as tabulated files, as images, as PDF and/or
 as static HTML)
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Authors
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Gitools has been conceived by Nuria López-Bigas and the architecture and
 most of the programming has been done by Christian Pérez-Llamas.
 Other people has contributed too, Jordi Deu-Pons with the interface to
 import IntOGen data and Xavier Rafael-Palou improving the interface with
 Biomart.
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Contacting
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Gitools web is at
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https://www.gitools.org
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There you will find how to subscribe to the newsletter to be updated with
 the last news regarding Gitools.
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For suggestions or bug reports you can email 
\emph on
christian.perez@upf.edu
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.
 Please remember to include the error description and give instructions
 on how to reproduce the error when reporting bugs.
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\begin_layout Section
Acknowledgements
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Gitools is being developed under the grants of the Ministry of Science of
 Spain and Human Frontiers Science Program.
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It is also important the feedback received from users, specially our early
 bug reporters: Khademul Islam, Alba Jené-Sanz and Gunes Gundem.
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License
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The Gitools distribution is licensed according to
\emph on
GNU GPL 3.0
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.
 See the files in the top-level of the Gitools distribution called 
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LICENSE.txt
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 and see licenses for accompanying products in the "
\emph on
lib
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" directory.
 See full explanation and FAQs regarding the GNU GPL 3.0 License at
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http://www.gnu.org/licenses/
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