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| − | == Feature requests for geWorkbench ==
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| − | === General Features ===
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| − | * Mantis 0000114: Persisting configuration settings designated through the visual builder
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| − | At present, changes to the start up configuration effected during the
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| − | application execution (through the Visual Builder) do not get persisted: when
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| − | the application is launched the original start up configuration is used again.
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| − | It is desirable that changes introduced by the Visual Builder be persisted in
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| − | the application's configuration file so that they can be "remembered" at the
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| − | next launch.
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| − |
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| − | * Mantis 0000115: Choosing among available application "flavors"
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| − | During application launch, a start up window (which the user can opt to hide
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| − | for subsequent application invocations) should prompt the user to select one
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| − | among the available application configuration "flavors". This functionality
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| − | should be available not only at start up but also from within the application,
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| − | through a "Preferences" type of menu option.
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| − |
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| − | * Mantis 0000077: Context sensitive online help
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| − | We need to make online help available in a context sensitive manner: from
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| − | within a component, a user should be able (using F1 or by pressing a Help
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| − | button) get access to the online help associated with the component.
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| − |
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| − | === Menu ===
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| − | * Mantis 0000166: main menubar controls for Project Folders Area are confusing.
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| − | The problem is caused by the differences in type and semantics between workspace
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| − | folder and project folders. For example, The "File" submenu offers "Open" and
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| − | the pop-up choices are "File" or "Workspace". Select Workspace and you are
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| − | offered a dialog box. Select "File" and you are told you must first select a
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| − | project node. Or if you select "New" (an adjective) from the submenu, you get a
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| − | choice of "Workspace" or "Project". Select "Workspace" and the current workspace
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| − | folder is cleared of its contents. Thus New Workspace actually REMOVES the
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| − | Workspace folder, whereas the submenu item "Remove" does not include "workspace"
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| − | as an option. Select "Project" and a new project folder is added without
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| − | replacing an existing one. I think the whole thing could be made more obvious
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| − | and logical by making the File submenu items "Workspace" and "Projects" and
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| − | perhaps "Files". Then the choices under each could be actions (verbs) - e.g
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| − | Open, Remove, Load, Delete, Save, etc. In other words, you consider the folder
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| − | that you want to do something to, select it in the file menu and choose the
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| − | action that you want to take. Also the other file items "Export" etc. have
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| − | nothing to do with the Project Folders Area and are positioned awkwardly.
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| − | ----
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| − | ==== File ====
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| − | ----
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| − | ==== Edit ====
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| − | ----
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| − | ==== View ====
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| − | ----
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| − | ==== Commands ====
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| − | ----
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| − | ==== Tools ====
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| − | ----
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| − | ==== Help ====
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| − |
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| − | ----
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| − | ----
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| − |
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| − | === Project Folders ===
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| − |
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| − | ----
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| − | ----
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| − |
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| − | === Markers ===
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| − |
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| − | ----
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| − | ----
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| − |
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| − | === Arrays/Phenotypes ===
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| − |
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| − | ----
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| − | ----
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| − |
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| − | === Sets ===
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| − |
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| − | ----
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| − | ----
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| − |
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| − | === FASTA sequences ===
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| − | ==== Promoter ====
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| − | ----
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| − | ==== Sequence Panel ====
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| − | ----
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| − | ==== Position Histogram ====
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| − | ----
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| − | ==== Simulation ====
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| − | ----
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| − | ===== Network Generator =====
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| − | ----
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| − | ===== Phenotype & Optimizer Options =====
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| − | ----
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| − | ===== Interactions Display =====
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| − | ----
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| − | ==== 5. Sequence alignment ====
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| − | ----
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| − | ===== BLAST =====
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| − | ----
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| − | ===== HMM =====
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| − | ----
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| − | ===== Other =====
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| − | ----
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| − | ==== Pattern discovery ====
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| − | ----
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| − | ==== Associations ====
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| − | ----
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| − | ==== caScript ====
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| − | ----
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| − | ==== Dataset annotations ====
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| − | ----
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| − | ==== data history ====
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| − | ----
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| − | ==== Experiment Info ====
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| − |
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| − | ----
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| − | ----
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| − |
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| − | === '''Microarray data''' ===
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| − | The following panels/functionalities are requested specifically for Microarray data:
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| − | *
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| − | ==== Simulation ====
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| − | ----
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| − | ==== Network browser ====
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| − | ----
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| − | ==== Interactions ====
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| − | ----
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| − | ==== Aracne ====
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| − | ----
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| − | ==== Tabular Microarray Viewer ====
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| − | ----
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| − | ==== Sequence Retriever ====
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| − | ----
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| − | ==== Synteny ====
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| − | ----
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| − | ==== Microarray viewer ====
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| − | ----
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| − | ==== Gene Ontology ====
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| − | ----
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| − | ==== GSEA ====
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| − | ----
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| − | ==== Reverser Engineering ====
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| − | ----
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| − | ==== Scatter Plot ====
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| − | ----
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| − | ==== caBIO pathways ====
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| − | ----
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| − | ==== Marker Annotations ====
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| − | ----
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| − | ==== Color Mosaic Expression Profiles ====
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| − | ----
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| − | ==== Expression Value Distribution ====
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| − | ----
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| − | ==== Experiment Info ====
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| − | ----
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| − | ==== Synteny Parameters ====
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| − | ----
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| − | ===== Program =====
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| − | ----
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| − | ====== MUMmer ======
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| − | ----
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| − | ====== Dots ======
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| − | ----
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| − | ====== Synteny map ======
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| − | ----
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| − | ===== Genome selections =====
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| − | ----
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| − | ===== Annotations =====
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| − | ----
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| − | ==== Normalization ====
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| − | ----
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| − | ===== Housekeeping Genes Normalizer =====
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| − | ----
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| − | ===== Log2 Transformation =====
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| − | ----
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| − | ===== Marker-based centering =====
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| − | ----
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| − | ===== Mean-variance normalizer =====
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| − | ----
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| − | ===== Array-based centering =====
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| − | ----
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| − | ===== Missing value computations =====
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| − | ----
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| − | ===== Threshold Normalizer =====
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| − | ----
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| − | ===== Quantile Normalization =====
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| − | ----
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| − | ==== T-Profiler ====
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| − | ----
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| − | ==== Analysis ====
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| − | The following analysis functions are requested:
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| − | * ANOVA
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| − | ----
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| − | ===== Fast Hierarchical clustering =====
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| − | ----
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| − | ===== Matrix reduce =====
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| − | ----
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| − | ===== Svm classifier =====
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| − | ----
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| − | ===== Slmr classifier =====
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| − | ----
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| − | ===== SOM =====
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| − | ----
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| − | ===== T-test =====
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| − | ----
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| − | ===== Multi T-test =====
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| − | ----
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| − | ==== Associations ====
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| − | ----
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| − | ==== caScript ====
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| − | ----
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| − | ==== Dataset Annotations ====
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| − | ----
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| − | ==== Filtering ====
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| − | ----
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| − | ===== Deviation filter =====
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| − | ----
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| − | ===== Affy detection call filter =====
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| − | ----
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| − | ===== Expression threshold filter =====
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| − | ----
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| − | ===== Genepix flags filter =====
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| − | ----
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| − | ===== Missing value filter =====
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| − | ----
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| − | ===== 2 channel threshold filter =====
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| − | ----
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| − | ==== Dataset History ====
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| − | * Mantis: 0000300: need array info
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| − | We should be able to display information about a microarray - the chip type, the
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| − | number of markers in the dataset vs in the chip definition.
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| − |
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| − | ----
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