.. _indices:

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Welcome to PathLay's documentation!
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* :ref:`Features <features>`
* :ref:`Requirements <requirements>`
	* :ref:`For Building the Docker Image <requirements_docker>`
	* :ref:`For the Apache Server Installation <requirements_apache>`
* :ref:`Installation <installation>`
	* :ref:`Installation on Linux <installation_linux>`
		* :ref:`Building the Docker Image <installation_docker>`
		* :ref:`Installing from Deb <installation_deb>`
		* :ref:`Apache Server Installation <installation_apache>`
* :ref:`How to Run<howto>`
	* :ref:`Run PathLay as Server <howto_docker_server>`
* :ref:`Usage <usage>`
	* :ref:`Account Managing <usage_account>`
		* :ref:`Register a New Account <usage_account_new>`
		* :ref:`Login to an Existing Account <usage_account_login>`
	* :ref:`Experiment Package <usage_specs>`
		* :ref:`Configuration File <usage_specs_conf>`
		* :ref:`Datasets Files <usage_specs_data>`
		* :ref:`Supported IDs <usage_specs_ids>`
	* :ref:`Home Manager <usage_home>`
		* :ref:`Creating an Experiment Package <usage_home_create>`
		* :ref:`Loading an Experiment Package <usage_home_load>`
		* :ref:`Gene Ontologies <usage_home_ont>`
		* :ref:`Downloading an Experiment Package <usage_home_download>`
	* :ref:`Configuration Page <usage_access>`
		* :ref:`Maps Databases <usage_access_mapdb>`
		* :ref:`Maps Restriction Procedure <usage_access_stat>`
		* :ref:`Data Selection <usage_access_data>`
		* :ref:`Configuring a Dataset <usage_data_types>`
		* :ref:`Filtering Options <usage_data_filters>`
		* :ref:`ID Preservation <usage_data_id_only>`
		* :ref:`Non Differentially Expressed IDs <usage_access_nodeg>`
		* :ref:`Transcription Factors <usage_access_tfs>`
		* :ref:`Transcription Factors ID Preservation <usage_access_id_only_tfs>`
		* :ref:`Loading Non Differentially Expressed IDs from TFs <usage_access_no_de_tfs>`
	* :ref:`Pathway Explorer <usage_results>`
		* :ref:`Pathway Navigation <usage_results_mapsel>`
		* :ref:`Indicators <usage_results_legend>`
		* :ref:`Main Menu <usage_results_menu>`
		* :ref:`Highlighting Feature <usage_results_highlight>`
		* :ref:`The Clipboard <usage_results_clipboard>`
		* :ref:`The Logical Section <usage_results_logical>`
			* :ref:`Select by IDs <usage_results_logical_byids>`
			* :ref:`Select by Agreement <usage_results_logical_byagreement>`
		* :ref:`Settings <usage_results_settings>`
			* :ref:`Transparency and Size <usage_results_settings_transparencyandsize>`
			* :ref:`Screenshot <usage_results_settings_screenshot>`
* :ref:`Contribute <contribute>`
* :ref:`Support <support>`
* :ref:`License <license>`