PIPAx
=====

![Widget icon](icons/pipax.png)

Gives access to [**PIPA**](http://pipa.biolab.si/hp/index.html#) databases.

Signals
-------

**Inputs**:

- (None)

**Outputs**:

- **Data**

  Selected experiments. Each annotated column contains results
  of a single experiment or, if the corresponding option is
  chosen, the average of multiple replicates.

Description
-----------

**PIPAx** is a widget for a direct access to [**PIPA**](http://pipa.biolab.si/hp/index.html#) database.
It is very similar to the **GenExpress** and **GEO Data Sets** widgets as it allows you to download the data from 
selected experiments.

![PIPA widget](images/PIPAx-stamped.png)

1. Reloads the experiment data.
2. The widget will save (cache) downloaded data, which makes them also available offline. To reset the widget click *Clear cache*.
3. Use *Experiment Sets* to save a selection:
   select the experiments, click the "**+**" button and name the
   set. To add experiments to the set, click on its name, select
   additional experiments and click *Update*.<br>To remove the set click "**-**".
4. In *Sort output columns* set the attributes by which the output columns are sorted.
   Add attributes with a "+" button and remove them
   with "-". Switch the sorting order with arrows on the right.
5. Set the expression type for your output data.
   - **Raw expression** outputs raw experiment data
   - **RPKM expression** outputs data in *reads per kilobase of transcript per million mapped reads*
   - **RPKM expression + mapability expression** uses similar normalization, but divides with gene 
     mapability instead of exon lengths.<br>The polyA variants use only polyA (mRNA) mapped hits.
6. **Exclude labels with constant values** removes attribute labels that are the same for all selected 
    experiments from the output data.<br>
   **Average replicates (use median)** averages identical experiments by using medians as values.<br>
   **Logarithmic (base 2) transformation** computes the log<sub>2</sub>(value+1) for each value.
7. Click *Commit* to output selected experiments.
8. Log in to access private data.
9. Experiments can be filtered with the *Search* box.
   To select which attributes to display right-click on the header. To select multiple experiments 
   click them while holding the *Control/Command* key.

Example
-------

In the schema below we connected **PIPAx** to **Data Table**, **Set Enrichment**, and **Distance Map**
(through **Distances**) widgets.

![](images/PIPA-Example.png)

The **Data Table** widget above contains the output from the **PIPAx** widget.
Each column contains gene expressions of a single experiment. The labels
are shown in the table header. The **Distance Map** widget shows distances between experiments. The
distances are measured with **Distance** widget, which was set to
compute *Euclidean* distances.