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        "author": "Antti Honkela",
        "author_email": "antti.honkela@helsinki.fi",
        "bugtrack_url": null,
        "classifiers": [
            "Environment :: Web Environment",
            "License :: OSI Approved :: GNU Affero General Public License v3",
            "Natural Language :: English",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Topic :: Database :: Front-Ends",
            "Topic :: Internet :: WWW/HTTP :: Dynamic Content",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "tigreBrowser\n============\n\nGene expression model browser for results from tigre and GPrank R packages\n(http://www.bioconductor.org/packages/release/bioc/html/tigre.html),\n(https://cran.r-project.org/package=GPrank).\n\ntigreBrowser is licensed under GNU Affero General Public License (AGPL3)\n\ntigreBrowser includes jQuery 1.4.2. (http://jquery.com/) licensed under MIT/GPL2 license\n\ntigreBrowser includes jQuery Dynamic Form 1.0.3. (http://code.google.com/p/jquery-dynamic-form/) licensed under GPL3 license\n\n\nRecent changes\n==============\n\nVersion 1.1 (2017-02-10)\n* More robust file search for stand-alone version\n\nVersion 1.0.4 (2015-09-14)\n* CSS file reorganisation for more reliable operation on https servers\n\nVersion 1.0.3 (2014-01-28)\n* File reorganisation to simplify database import from text files\n* Add new options to control UI complexity\n\nVersion 1.0.2 (2011-09-20)\n* Fix a bug in handling '_' in experiment names\n\nVersion 1.0.1 (2011-01-17)\n* Miscellaneous bugfixes.\n\nVersion 1.0.0 (2010-10-08)\n* Initial release.\n\n\nInstallation\n============\n\ntigreBrowser requires Python version >=2.5.\ntigreBrowser can be installed with the following command:\n\n```\npython setup.py install\n```\n\nFor more information about installing python modules (for example, installing\nwithout root permissions for the current user only), see\nhttp://docs.python.org/install/\n\n\nStarting server\n===============\n\nThe web server included in tigreBrowser must be running in order to use the\nactual result browser.\n\nYou will need a database file generated by the tigre R package\n(http://www.bioconductor.org/packages/release/bioc/html/tigre.html) or the\nGPrank R package (https://cran.r-project.org/package=GPrank). The tigre\npackage contains a test database file 'database.sqlite' which can be used to\ntest tigreBrowser. The test database was generated using the instructions and\nexample data included in tigre package.\n\nExecute tigreServer.py to start the graphical user interface of the server. In\norder to start the result browser, one must first select a database file of\nwhich results will be shown. This can be accomplished by selecting 'Open\ndatabase file' and choosing a database file. The database file must not have\nwrite permissions. The server can then be started by clicking 'Start server'.\nWhen clicked, a label appears below the buttons to show the URL of the result\nbrowser.\n\nThe result browser is now accessible in that URL using a regular web browser.\nInstructions on using the browser are in the next section of this manual. The\nbrowser is available until the server is stopped with the 'Stop server' button.\n\ntigreServer.py can also be used with a command-line interface. Start the script\nwith `--help` option for more details.\n\n\nUsing the browser\n=================\n\nDataset selection\n-----------------\n\nThe dataset selection determines which results will be visible in the results\nlisting and in which order. The experiment set selection is used to select the\nset of experiments. Only results from these experiments will be shown in the\nlisting.\n\nNext in the dataset selection is the selection of transcription factor (TF) or\ntarget set, depending on whether the result browser is set to Target ranking\nmode or regulator ranking mode (see installation). In target ranking mode, the\nTF selection is available and the results listing contains results for\ndifferent targets with the given TF. In regulator ranking mode, the target set\nis selected and the listing will show results for different regulators.\n\nAs the number of results can be high, the results might be divided into multiple\npages. \"Number of genes per page\" selection can be used to adjust the number of\nshowed results. It can be useful to decrease the number of results if the page\nloads slowly due to huge number of images.\n\nFinally, the order in which the results are showed can be altered with the\n\"Sort by\" selection. The results will be sorted descendingly by the given\ncriterion.\n\n\nFiltering\n---------\n\nResults can be filtered by different criteria. One can, for example, show only\nresults for genes that have z-score higher than a certain threshold.\n\nIt is possible to combine multiple criteria when filtering. \"[+]\" link can be\nused to add another criterion. A criterion can be likewise removed using \"[-]\"\nlink (not showed when there is only one criterion). When multiple criteria are\nused, a gene result must meet all the criteria to be showed in the listing.\n\nFiltering is activated using \"Apply filters\" checkbox.\n\n\nHighlighting\n------------\n\nIf genes in the database contain supplementary data, results can be highlighted\nusing that data. The available highlighting options are showed with the colors\nassociated to those options.\n\nThe highlighting works by showing colored boxes below the probe names in the\nresult listing for genes which have supplementary data that matches the\nselection.\n\n\nSearch\n------\n\nIt is possible to search results for the given genes. The search works by\ntyping comma separated list of gene or probe names to the search box. Gene\naliases can also be used as a search entry.\n\n\nDisplaying results\n------------------\n\nThe results for the given selection of dataset, filters, highlights and search\nwill be showed when \"Send\" button is clicked. The database will then be queried\nfor results which match the given selection. \"Reset\" button can be used to\nclear all selections and textfields.\n\nThe results listing contains multiple columns. In the first column a probe\nname is displayed with a GENENAME associated with the probe. Next to the gene\nname, is the gene expression figure if one is defined in the database. The\nfollowing column contains the actual results for genes. Any supplementary data\nis also displayed here. Experiment figures will be displayed alongside the\nresult values.\n\nFinally, experiment parameters, if inserted into the database, will be\ndisplayed as a table next to the figures.",
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        "license": "AGPL3",
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        "name": "tigreBrowser",
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