Manage Data

This article will cover data management operations for the following data groups:

• Collections

• Samples

• Data objects

• Gene sets

Manage collections

Create new

A new collection can be created in the following ways:

• When you import new data to Genialis Expressions, a new collection is created automatically, unless you choose to assign the newly imported samples to an existing collection.

• A collection can also be created from scratch in the Collections tab on the Search for Data page. Click the ‘Create new collection’ icon button. A New Collection page will appear prompting you to give it a name, an URL slug and a short description.

• When moving samples or data objects, a modal window will give you the option to either move the selected samples or data objects to an existing collection or to create a new one. If you opt for the latter you’ll only need to enter a name for the new collection and click on the ‘MOVE’ button.

Edit/Modify

You can modify a collection name, URL slug and description in the General Settings card on the Collection Settings page. Make sure to save all new changes at the end by clicking the ‘SAVE’ button.

The Collection Settings page will appear by clicking on the ‘COLLECTION SETTINGS’ button found at the top right of the View Collection Details page.

Share

You can share and manage permissions for a specific collection (and subsequently for all its corresponding samples and data objects.) in the Permissions card on the Collection Settings page. The Collection Settings page will appear by clicking on the ‘COLLECTION SETTINGS’ button found at the top right of the View Collection Details page.

The Permissions card displays all users and groups that have access to this collection and their level of permissions. The current permissions levels for all the invited Users and Groups are listed under the ‘Who has access’ section, ranging from ‘Owner’ with full access and moving down through ‘Share’, ‘Edit’, and ‘View’ which is the lowest level of access. There is also an option to set the Public access which only has two permission levels: ‘View’ and ‘Off’.

Manage permissions:

• New users/groups can be invited by using the invite forms and clicking the ‘INVITE’ button. You’ll need to know the exact name of the user or group to share data. If you are not sure, please contact support@genialis.com for assistance.

• Permission levels for existing users/groups can be changed by selecting a different level from the dropdown and clicking the ‘SAVE’ button.

• You can completely revoke permissions for existing users and groups by removing them from the list by clicking on the ‘X’ icon button next to the user/group name. Public access entry can’t be removed - you can simply select ‘Off’ from the dropdown menu next to it if you don’t wish for your data to be publicly available for all Expressions users. ‘Off’ is also the default Public permission level for all new data.

Delete

You can delete an entire collection using one of these two options:

• If you click the ‘DELETE COLLECTION’ button in the Danger Zone card on the Collection Settings page (reached through View Collection Details page).

• If you select the collection in the results table of the Collections tab on the Search for Data page and then click on the ‘Delete’ icon button.

Both options will prompt you to confirm your intention. Deleting a collection will also delete all its corresponding samples and data objects. Be sure to use this option with caution, as there is no coming back once you delete something.

Manage samples

Create new

New samples are created automatically when you use the Import Data page to upload your raw files. Alternatively, you can use any of the import tools in the ’Tool Catalog’ tab within the Actions card on the View Collection Details page. This is particularly useful if you want to create a new sample with a BAM file or an expressions file, for example.

Edit/Modify

You can modify a sample by changing its metadata. For more information see the Annotate Samples article.

Duplicate

You can duplicate a sample using one of these two options:

• If you select the sample in the results table of the Samples tab on the Search for Data page and then click on the ‘Duplicate’ icon button.

• If you select the sample in the Samples card on the View Collection Details page and then click on the ‘Duplicate’ icon button.

Note that in order to duplicate a data object you must have the ‘Edit’ permission on the collection the sample belongs to.

Reanalyzing samples

A common request is to be able to analyze raw data with an alternative pipeline. If you simply ran an alternative pipeline on selected samples, you’d end up with two sets of results on each sample (e.g. two BAM files, two expression tables, etc.). Unfortunately such samples cannot be viewed in visualizations as there is no way to instruct the visualization modules which set of results to use. For that reason, a preferred way to re-analyse data is to first duplicate a sample, delete all but the raw reads from that duplicated sample, and only then run the alternative pipeline. In that way, you’ll end up with samples that you can directly compare within visualizations.

Move

You can move samples from one collection to another using one of these two options:

• If you select the sample in the results table of the Samples tab on the Search for Data page and then click on the ‘Move’ icon button.

• If you select the sample in the Samples card on the View Collection Details page and then click on the ‘Move’ icon button.

Both options will result in a Move to collection modal window appearing. It will prompt you to either select an existing collection or create a new collection where you want to move the sample to. The action will be completed by clicking on the ‘MOVE’ button.

Note that in order to move a sample you must have the ‘Edit’ permission on the collection this sample currently belongs to and the collection you are moving it to.

Delete

You can delete a sample using one of these two options:

• If you select the sample in the results table of the Samples tab on the Search for Data page and then click on the ‘Delete’ icon button.

• If you select the sample in the Samples card on the View Collection Details page and then click on the ‘Delete’ icon button.

You will be prompted to confirm. Be sure to use this option with caution, as there is no coming back once you delete something. Note that in order to move a sample you must have the ‘Edit’ permission on the collection the sample belongs to.

Manage data objects

Create new

A new data object is created in one of the following ways:

• It is created automatically when you import new data to Genialis Expressions

• As a result of an analysis that has been run

• By using one of the import tools in the ‘Tool Catalog’ tab within the Actions card on the View Collection Details page.

Edit/Modify

You can edit the data object’s name or URL slug on the View Data Object Details page. The Data Object Details page can be accessed by clicking on a data object name either:

• in the results table from Data Objects tab on the Search for Data page or

• in the Data Objects card from within the View Collection Details page.

Duplicate

You can duplicate a data object using one of these two options:

• If you select the data object in the results table of the Data Objects tab on the Search for Data page and then click on the ‘Duplicate’ icon button.

• If you select the data object in the Data Objects card on the View Collection Details page and then click on the ‘Duplicate’ icon button.

Note that in order to duplicate a data object you must have the ‘Edit’ permission on the collection this data object belongs to.

You can only duplicate data objects that have not been created as a result of sample analysis and are therefore not part of any particular sample.

Move

You can move data objects from one collection to another using one of these two options:

• If you select the data object in the results table of the Data Objects tab on the Search for Data page and then click on the ‘Move’ icon button.

• If you select the data object in the Data Objects card on the View Collection Details page and then click on the ‘Move’ icon button.

Both options will result in a ‘Move to collection’ modal window appearing. It will prompt you to either select an existing collection or create a new collection where you want to move the data object to. The action will be completed by clicking on the ‘MOVE’ button.

Note that in order to move a data object you must have the ‘Edit’ permission on the collection this data object currently belongs to and the collection you are moving it to.

You can only move data objects that have not been created as a result of sample analysis and are therefore not part of any particular sample.

Delete

You can delete a data object using one of these two options:

• If you select the data object in the results table of the Data Objects tab on the Search for Data page and then click on the ‘Delete’ icon button.

• If you select the data object in the Data Objects card on the View Collection Details page and then click on the ‘Delete’ icon button.

You will be prompted to confirm. Be sure to use this option with caution, as there is no coming back once you delete something. Note that in order to delete a data object you must have the ‘Edit’ permission on the collection you are working in.

Manage gene sets

Create new

You can create a new gene set using one of the following two options:

• From the Gene Basket: After populating the Gene Basket click on the ‘Save a gene set’’ icon button. This will open a new panel called Gene Set Settings. Here you can give your gene set a name and a description. Once saved (by clicking the ‘SAVE & CLOSE’ button), this gene set can be loaded for use again in the future.

• From a Venn diagram: From the Gene Basket select up to 4 gene sets and click on the ‘Open Venn diagram tool’ link. After the Venn diagram appears in the Venn diagram tool panel select the desired areas in a Venn diagram and click on the ‘SAVE A GENE SET’ button at the bottom of the panel. This will open a new Gene Set Settings panel. Here you can give your gene set a name and a description. Once saved (by clicking the ‘SAVE & CLOSE’ button), this gene set can be loaded for use again in the future.

The rest of the gene set handling is performed through the Gene Basket panels. Open the Gene Basket and click on the ‘Show gene set settings’ icon button next to the gene set name. This will open the Gene Set Settings panel where you will be able to manage the following:

Edit

Update the gene set name and description in the appropriate input fields

Share

The current permissions levels for all the invited Users and Groups are listed under the ‘Who has access’ section, ranging from ‘Owner’ with full access and moving down through ‘Share’, ‘Edit’, and ‘View’ which is the lowest level of access. There is also an option to set the Public access which only has two permission levels: ‘View’ and ‘Off’.

• New users/groups can be invited by using the invite forms and clicking the ‘INVITE’ button. You’ll need to know the exact name of the user or group to share data. If you are not sure, please contact support@genialis.com for assistance.

• Permission levels for existing users/groups can be changed by selecting a different level from the dropdown

• You can completely revoke permissions for existing users and groups by removing them from the list by clicking on the ‘X’ icon button next to the user/group name. Public access entry can’t be removed - you can simply select ‘Off’ from the dropdown menu next to it if you don’t wish for your data to be publicly available for all Expressions users. ‘Off’ is also the default Public permission level for all new data.

Duplicate

Duplicate a gene set by clicking on the ‘Duplicate gene set’ icon button. A copy will appear in the Gene Basket list.

Delete

Delete a gene by clicking on the ‘Delete gene set’ icon button. Be sure to use this option with caution, as there is no coming back once you delete something.

Note that all changes must be confirmed by clicking the ‘SAVE & CLOSE’ button at the bottom of the Gene Set Settings panel.