perturbation_effect
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perturbation_effect [2020/01/27 21:15] krian |
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| The **Perturbation effect module** can be accessed from the main menu bar, by clicking on the //Perturbation effect// button. | The **Perturbation effect module** can be accessed from the main menu bar, by clicking on the //Perturbation effect// button. | ||
| {{ :perturbation_effect_form.png?nolink |}} | {{ :perturbation_effect_form.png?nolink |}} | ||
| - | ===== INPUT ===== | + | ===== Perturbation effect form ===== |
| - | + | The main page of the tool is a form. This form includes all the information and parameters needed to process a perturbation effect study. | |
| - | The main page of the tool is a form. This form includes all the information and parameters needed to process a perturbation effect study. The form is divided in different panels: | + | {{ ::perturbationeffectform.png?nolink |}} |
| + | The form is divided in different panels: | ||
| ==== Expression matrix file ===== | ==== Expression matrix file ===== | ||
| * **[[Expression matrix file format |Expression matrix file]]** : Expression matrix provided by ourselves (see how to upload files in [[upload_your_data|Upload your data]]). | * **[[Expression matrix file format |Expression matrix file]]** : Expression matrix provided by ourselves (see how to upload files in [[upload_your_data|Upload your data]]). | ||
| + | {{ ::expmatrfile.png?nolink |}} | ||
| + | When we select a gene expression file, the number of samples of this matrix will appear under the “File browser” button as shown below. | ||
| + | {{ ::pertnumberofsamples.png?nolink |}} | ||
| ==== Sample ==== | ==== Sample ==== | ||
| Once the file is selected the column names of the expression matrix will be loaded in this panel, we have to select the column to proceed. | Once the file is selected the column names of the expression matrix will be loaded in this panel, we have to select the column to proceed. | ||
| - | {{ :persurbationeffect.png |}} | + | {{ ::samplesperteffectform.png?nolink |}} |
| ==== Study information ==== | ==== Study information ==== | ||
| - | For further information about this panel, see [[job information|Study information ]] | + | This panel includes some parameters in order to identify and save our study. |
| + | * **Output folder**: If we want to reorganize our studies we can select the folder in which we want save our report. By default the study will be saved in the home in a folder named "Perturbation_effect_study-N", N is an integer number. | ||
| + | * **Study name**: We can give a name to our study. This is very useful to later identify it among the other studies listed in the //My studies// list.\\ The default study name is "Perturbation_effect_study-N", N is an integer number. | ||
| + | * **Description**: We can give a description to our study. | ||
| + | {{ ::studyinfopereffectform.png?nolink |}} | ||
| + | ==== Run analysis ==== | ||
| + | Once the form has been filled in, press the //Run analysis// button to launch the study. Your study will be listed in the //My studies// panel. | ||
| + | {{ ::runanalysis.png?nolink |}} | ||
| + | Your study will be listed in the //My studies// panel, and a panel called //Browse my studies// will appear showing all your studies and their state. the new study will appear with a **queued** state then **running** state. If everything goes well, the state will be **done** after few minutes(depending on the inputs data and the availability of server). | ||
| + | All study states are: | ||
| + | * **Queued**: The information has been processed and the study has been sent and waits to be processed. | ||
| + | {{ ::queuedpereff.png?nolink |}} | ||
| + | * **Running**: The study is in progress, study can be cancelled using the stop button. | ||
| + | {{ ::runingperteffect.png?nolink |}} | ||
| + | * **Done**: The study has ended and the results are available to visualize and download. | ||
| + | * **Cancelled**: The study was canceled before finishing. | ||
| + | * **Error**: Sometimes a study can stop returning a error message, you can report and contact us in order to help you to fix it. | ||
| + | {{ ::studiesperteffect.png?nolink |}} | ||
| - | Once the form has been filled in, press the //Run analysis// button to launch the study. Your study will be listed in the //My studies// panel. | ||
| - | ===== OUTPUT ===== | + | ===== Perturbation effect report ===== |
| The results page of the Perturbation effect tool is an ** interactive working environment **. You can **simulate knock outs or over-expressions of one or several genes ** or the ** effect of a drug** in the activity of signaling pathways. | The results page of the Perturbation effect tool is an ** interactive working environment **. You can **simulate knock outs or over-expressions of one or several genes ** or the ** effect of a drug** in the activity of signaling pathways. | ||
perturbation_effect.1580159707.txt.gz · Last modified: 2020/04/03 20:18 (external edit)
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