CoV-HiPathia

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====== Variant Interpreter ======
The Variant interpreter allows us to infer how a gene (or combination of genes) knockdown may deregulate the signaling pathways activity. This impact is evaluated by comparing the normal activity values from a given tissue, with the activity values of that same tissue calculated after the //in silico// knockdown of the expression values of the genes of interest. 

This can be done for each signaling pathwat and for each one of the tissues included in GTEx. Additionally, the user can upload a file with gene expression data to perform the analysis on custom tissue.

Essentially, we are comparing pathway activities between two groups (Normal tissue Vs Knockdown tissue), to aid us in the functional interpretetion of disruptive genomic variants.
 
The tool can be accessed from the upper main menu bar, by clicking on the //Variant interpreter// button. See [[workflow|Workflow]] for further information.
{{ :vafin_form.png?nolink |}}
===== Variant interpreter form =====
The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to carry out the analysis. The form is divided in different panels:
==== Input data panel ====
{{ ::inputdatavafinform.png?nolink |}}
A tabulated text file with data on genomic variation must be uploaded. This file must include list of gene names in HUGO or entrez id (see [[http://hipathia.babelomics.org/doc/doku.php?id=gene_list_file_format|gene list file forma]]t for more information).This genes list corresponds to the genes to in silico knockdown simultaneously.\\ 
Then you have to select at least one tissue, or a custom matrix file has to be loaded after checking the "Search for custom tissue" checkbox as shown below:
{{ ::checkedsearchforcustomtissue.png?nolink |}}
**Note**: You can select all options, but you have to take into account that the analysis will take more minutes depending on you custom tissue file and the server availability.
==== Pathways ====
This panel includes the list of all available pathways in HiPathia. We can select the pathways with which the analysis will be performed.\\ HiPathia retrieves pathway information from [[https://www.kegg.jp/kegg/pathway.html|KEGG database]]. KEGG pathway database is a collection of manually drawn pathway maps representing the knowledge on the molecular interaction, reaction and relation networks. 
{{ :pathways.png?nolink |}}
By default all available pathways are selected.\\ **Note:** At least one pathway has to be selected.
==== 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 "VaFI_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 "VaFI_study-N", N is an integer number.
  * **Description**: We can give a description to our study.
{{ ::studyinfovafinform.png?nolink |}}

==== Run analysis ====
Once the form has been filled in, press the //Run analysis// button to launch the study. 
{{ ::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.
  * **Running**: The study is in progress, study can be cancelled using the stop button.
{{ ::vafintocancelled.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.
{{ ::studiesvafin.png?nolink |}}

===== Variant interpreter report =====

The results page of the Variant Functional Interpreter tool ........ You can download the pathway.

  * [[Pathway viewer|Pathway viewer]]
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