rbbt-rest 1.2.35 → 1.2.36
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- checksums.yaml +8 -8
- data/share/views/compass/help.sass +4 -6
- data/share/views/help.haml +25 -11
- data/share/views/help/UI.haml +41 -39
- metadata +2 -2
checksums.yaml
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---
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!binary "U0hBMQ==":
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metadata.gz: !binary |-
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data.tar.gz: !binary |-
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NDU5MDA1OWVmNGVhZjBhZDc4YTdmMDdjMjg3MjllNTI1ZWY5N2MzMw==
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SHA512:
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metadata.gz: !binary |-
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data.tar.gz: !binary |-
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MGFlZDQzZTA1MTNjYWFiNjYyMWM0MmQ4ZDY3NzMxMmI5YTVkYzc=
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@@ -3,15 +3,13 @@ a.help
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display: block
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.UI
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dd
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.description, .images
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+grid-column(6, $float:left)
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& > dd
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+grid-row()
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& > .description, .images
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@media #{$only-large}
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+grid-column(6, $float:left)
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@media #{$not-large}
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width: 100%
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& > .images > dl
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& > dt
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data/share/views/help.haml
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@@ -2,29 +2,41 @@
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##Overview
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This application is designed for integration of data and functionalities.
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unambiguously identified and be subject of investigation. Examples of
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This application is designed for the integration of data and functionalities.
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Its design is based on the idea of the `Entity`: anything that can be
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unambiguously identified, and be subject of investigation. Examples of
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entities are: genes, proteins, SNPs, samples, pathways, etc.
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Each entity has a report, which depends on the type of entity it is.
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Each entity has a report, which depends on the type of entity it is. All
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reports are computed on the fly and cached. In addition to the main reports,
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entities have `actions`, which are sub-reports that implement particular
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analysis. For instance, for gene entities
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analysis. For instance, for gene entities one of the actions is to display a
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summary of the relevance of that gene across the collection of studies that
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you have access to. In addition to entities, there are reports for lists of
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entities and for entity maps, which are tables that relate entities to
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such as genes to their average mutation frequency.
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entities and for entity maps, which are tables that relate entities to
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values, such as genes to their average mutation frequency.
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##Important definitions
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Its common to think of coding variants as synonymous or non-synonymous. We
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find that this distinction is slightly inappropriate; a variant might be
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synonymous and still have a consequence in the protein isoform, for instance
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variants affecting exon junctions and that might interfere with splicing.
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Isntead of this nomenclature we prefer to talk about `relevant` and `not
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relevant` variants. Our current definition of `relevant` are variants that
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can potentially alter the function of at least one of the isoforms of a gene;
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this currently includes non-synonymous variants and variants affecting
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splicing sites (-2 to 8 bases of the donor end and -8 to 3 bases of the
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acceptor end).
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:markdown
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##User interface
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The user interface offers a general structure for all reports that allows to
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enact workflows, explore the results and connect functionalities with one
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another.
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another. This web site is 'responsive', meaning that it adapts to the size
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of the device you are using: computer, tablet, or phone. On small devices many
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of the layout elements shift around or get hidden behind toggle buttons to
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-
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accommodate themselves better to the screen size. The examples bellow are taken
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from a computer screen.
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=partial_render('help/UI')
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core functionalities through the Workflow subsystem. This is the same
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interface that is used as a REST web server, so it serves to document it.
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-
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%table
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%caption Available workflows on this site
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%thead
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%tr
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%th Workflow
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%th Description
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%tbody
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- Sinatra::RbbtRESTWorkflow::WORKFLOWS.each do |workflow|
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- next if workflow.asynchronous_exports.empty? and workflow.synchronous_exports.empty? and workflow.exec_exports.empty?
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No description
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- else
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= description.split("\n\n").first
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data/share/views/help/UI.haml
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This application presents reports for individual entities, lists of
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entities, and entity maps. Each type of entity (gene, study, pathway, etc.)
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has its own report template, and they are prepared on
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has its own report template, and they are prepared on-demand.
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All reports have the same overall structure; the images show a report
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for a genotyping study from the ICGC project. The top-bar is always
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there and provides a placeholder for several functionalities, most
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importantly the control of `favourites`.
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-
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Bellow the top-bar comes the report itself. It consists of a title, a
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side-bar, a description, and an `action controller`. In general the
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side-bar is used to show general meta-data about the entity and the
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description to show a brief overview.
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The action controller offers access to `actions
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The action controller offers access to `actions`, which are like
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sub-reports. Each type of entity has its own actions. If the entity
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type in particular does not have any action defined the action
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type in particular does not have any action defined then the action
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controller will not be displayed. When an action is selected, it will
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be displayed below, in the area called action loader.
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Actions can also be opened in their own page,
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Actions can also be opened in their own page, clicking the
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middle-button like any link. These pages are like reports but with no
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action controller or side-bar
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.images
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%dl.tabs.active.show
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:markdown
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The top-bar provides access to several functionalities. Clicking on the
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title of the application will link to its front-page.
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the reload button in the browser as well. I'm planning to fix this.
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title of the application will link to its front-page. Next to it is
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the reload-button, which is used to force the server to recalculate a
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report, otherwise the report will be taken from a cache. This is
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useful when a report has given an error or when when it was updated
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somehow. *Note:* After a reload of the report, the browser might still
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try to get the file from its own cache, so you might need to use the
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reload button in the browser as well; I'm planning to fix this.
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Next is the `favourites` controls, which we will discuss shortly. After
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that there might be a search box, if the server was started with that
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functionality. This search box can be configured to identify any type
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of entity, but generally it is only genes.
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The final component of the top-bar, which I label "
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controls, which allows to login or logout, and the job bookmarks,
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latter.
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The final component of the top-bar, which I label "User", has the user
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controls, which allows to login or logout, and the job bookmarks, where
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bookmarked actions are kept. Also this help page. Will discuss
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bookmarking actions latter.
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.images
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%dl.tabs.active.show
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it. *Note:* New lists are not made favourite be default, you still need to
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click on the star once the report is shown.
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.images
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%dl.tabs.active.show
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%dt.next.show Snapshot
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%dd
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%img(src="/img/UI/favourites_wire.png")
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%dt.next Actions
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%dd
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.description
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action report consists of the content of the action, and optionally,
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parameter controls and an action description. When the action is loaded
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inside a report the parameter controls and description are hidden, but
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they can be shown using the action control buttons in the top left
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Actions can also be opened in their own report
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button.
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they can be shown using the action control buttons in the top left of
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the action controller. Actions can also be opened in their own report
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by right/middle clicking on its button.
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As with all reports, they are executed the first time they are
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requested and the result is cached for further access. The action
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For instance the "Enrichment" action of gene lists performs an
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over-representation based analysis of functional classes. The
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functional classes include several pathway databases, protein domains,
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gene ages, etc. If we where
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gene ages, etc. If we where interested primarily in performing enrichment
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analysis using GO biological process terms, we can use the paperclip
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button to set that configuration of parameters as default so that it
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button to set that configuration of parameters as default, so that it
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always uses it initially.
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Some actions may require a significant amount of time to compute. The
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action controller tries to reload the action periodically until it is
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completed
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completed (after a while it will stop insisting to not overload the
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server). Instead of having to wait on that page for it to finish, the
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user can click on the bookmark button, which will place a link in the
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"jobs" tab on the "Extra" menu of the top-bar, and come back to it
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later.
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table through the `filter` button. The filters are defined per-column,
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and can contain exact strings, regular expressions like
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`/(COMPLETE|PARTIAL) RESPONSE/i`, statements such as `> \< ==` or `!=`.
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And
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And columns containing entities they can be prefixed with the term
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`name:` to force the filtering to work over the human readible text of
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the entities e.g. `name:/SF3B\d+/` for a column containing 'Ensembl
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Gene ID'.
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When a column contains entities, these are usualy listed in the table
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some identifier like 'Ensembl Gene ID' for genes or 'GO Term
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displaying the table, it automatically substitutes
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links to their corresponding reports, and lists
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the `column` button allows the user to
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When a column contains entities, these are usualy listed in the table
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using some identifier like 'Ensembl Gene ID' for genes or 'GO Term
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IDs', etc. When displaying the table, it automatically substitutes
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these identifiers with links to their corresponding reports, and lists
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them by name. Additionally the `column` button allows the user to
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report the list of entities of any column or, if the first column is
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itselve an entity, it allows the user to report the `map` between the
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entities in this column and the values of any other column. Maps are
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generally used as inputs to actions and tools, but may have actions as
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well; gene maps have an action that performs a rank-based enrichment
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analysis (provided the Enrichment workflow is loaded in the
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server).
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The content of the table can be downloaded in two forms, as TSV files,
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which is the original source of the table, or as Excel files. When
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visualization for different types of data. For instance: the `Graph`
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workflow implements the `cytoscape` tool, which is used to display
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different kinds of entities connected through databases or analitical
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results
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results (defined as `knowledge_bases`, but that is a subject for
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another discussion); the `Structure` `jmol` tool displays mutations in
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the secondary and tertiary structures and complexes; and the `D3Js`
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workflow that implements a tool to display `d3js` interactive SVG
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figures. Alternative R is used through a native interface in Rbbt to
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figures. Alternative R is used through a native interface in Rbbt to
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display plots using `ggplot2`.
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These tools are used by different reports and actions. The `Graph`
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workflow for instance redefines the template for `Gene` lists to
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include a cytoscape plot to the description section of the report.
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-
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.images
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%dl.tabs.active.show
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metadata
CHANGED
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--- !ruby/object:Gem::Specification
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name: rbbt-rest
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version: !ruby/object:Gem::Version
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version: 1.2.
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version: 1.2.36
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platform: ruby
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authors:
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- Miguel Vazquez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2013-12-
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date: 2013-12-29 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rake
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