The dashboard at https://cytetype.nygen.io/dashboard is where you manage your reports, your API keys and your account. It needs a signed-in browser session: if you are not signed in, it sends you to the sign-in page first and brings you back afterwards. See Sign in and API keys.
Open the dashboard¶
Open the URL in a browser, or open it from your terminal or R session:
cytetype dashboardOpenCyteTypeDashboard()Both open the dashboard of the server you signed in to, or https://cytetype.nygen.io/dashboard when there is no saved sign-in. They also print the URL, so you can copy it when no browser opens.
The sidebar links to Chat, Reports, API keys and the documentation. At the bottom are the workspace switcher (only for members of an organization with an active license) and your account.
Workspaces¶
Every account has a personal workspace. If your account belongs to an organization with an active license, the sidebar also shows a workspace switcher with your organization (and your role in it) and Personal. The dashboard offers one organization per account: the one it joined first. The Reports, API keys and Account pages always show the selected workspace only.
| Personal workspace | Organization workspace | |
|---|---|---|
| Who has it | Every account | Members of an organization with an active license |
| Reports | Jobs submitted with your personal API keys | Jobs submitted with your organization’s API keys |
| API keys | Personal keys (cyt_p_...) that you create | Organization keys (cyt_...) that admins create |
| Usage counted against | Your personal rolling limits | The organization’s cluster quota |
| Visibility options | Private, Public | Private, Organization, Public |
The API key that submits a job decides its workspace. A job submitted with a personal key belongs to your personal workspace and counts toward your personal limits. A job submitted with an organization key belongs to the organization workspace and counts toward the organization’s quota. Browser sign-in with cytetype setup or SetupCyteTypeR() gives you a personal key, so to run jobs under your organization, use an organization key from an admin (see Sign in and API keys).
When an organization’s license expires, its workspace is no longer offered in the switcher.
Reports¶
The Reports page has two tabs. The first is the same in both workspaces:
My Reports: the reports you own in this workspace, whether you submitted them or they were transferred to you.
The second depends on the workspace:
Shared with Me (personal workspace): personal reports that other people shared with you by email.
Workspace Reports (organization workspace): other members’ reports with Organization or Public visibility, and their private reports that were shared with you.
Each row in My Reports shows the report name, the report ID (with a copy button), the status (Processing, Completed or Failed), the visibility, who it is shared with, the number of clusters, the creation date and the actions. The other tab shows the owner instead of the sharing details.
Open a report, Chat or target analysis¶
Each row has up to three buttons:
View opens the report in a new tab (see The CyteType report).
Chat opens Chat in a new tab with this run attached. It appears for completed reports only.
Target analysis opens the target analysis dialog. It appears for completed reports only.
Rename a report¶
In My Reports, click the report name, type the new name and press Enter (Esc cancels). Reports without a name show “Untitled”. You can also name a report when you submit it, with a title key in metadata (see Study context and metadata). Only the owner can rename a report.
Change the visibility¶
Click the edit icon next to the visibility badge, choose Private, Organization or Public, and click Save. Organization is offered only in the organization workspace. You can change the visibility in either direction at any time. Visibility and sharing explains what each level allows.
Share by email¶
Tick the reports to share and click Share, or click the Shared With cell of a single report.
Enter an email address and click Add (or press Enter). Repeat for more people.
Click Save Changes.
What happens next:
Each recipient gets view access and one email that links to every report newly shared with them in this save.
A recipient without a CyteType account is listed as Pending. The invite turns into access the first time they sign in with that address.
Sharing again with someone who already has access does not send another email.
Recipients need an institutional email address, the same rule as for signing in.
With several reports selected, the dialog only adds people. To remove someone, including a pending invite, open the dialog for that one report, remove the address and click Save Changes.
Only the owner can share a report. Owners can also share from the Share button on the report page.
Transfer ownership¶
Transfer is available in the organization workspace only.
Tick the reports and click Transfer.
Enter the new owner’s email address and click Transfer All.
Confirm.
The new owner must be a member of the same organization. A transfer cannot be undone: the new owner gets all owner rights (rename, visibility, sharing, deletion) and you lose them. If the report is private, you also lose access to it unless the new owner shares it with you or sets it to Organization.
Archive a report¶
Tick the reports and click Archive. Archived reports disappear from the list until you tick Show archived; select them there and click Unarchive to bring them back.
Archiving does not change who can open the report: the link keeps working for everyone who could open it before. It removes the report from your lists, and from the report search in Chat and the job list of the MCP connector for everyone. An archived report can still be attached in Chat or connected through MCP by its full report ID.
Delete a report¶
Tick the reports in My Reports, click Delete and confirm. Only the owner can delete a report.
Deletion is a soft delete:
It cannot be undone from the dashboard. Deleted reports stay in My Reports under Show deleted, without any actions.
Everyone loses access, including you. All shares and pending invites are removed, and anyone who opens the link sees “Report Deleted: This report has been deleted by the owner.”
Requests for its results with an API key fail with the error code
REPORT_DELETED.Chat and the MCP connector can no longer use it. Chat answers and outputs that were based on it become unavailable.
Deleted jobs still count toward your usage limits or your organization’s quota (see Usage limits and quotas).
If you delete a report that is still processing, it disappears from your views but the job keeps running on the server until it finishes.
API keys¶
API keys let the Python and R clients submit jobs and fetch results. The API keys page lists the keys of the selected workspace.
Create a key¶
Select the workspace the key is for.
Click Create API key.
Enter a Key name, for example the computer or pipeline that will use it.
Optionally enter a Quota limit: the maximum number of clusters this key can annotate in total. Leave it empty for no per-key limit. Your other limits still apply.
Organization admins can enter a member’s address in User email (optional) to create the key for that member.
Click Create API key, then copy the key from the API key created panel.
To use the key, save it with cytetype login or LoginCyteTypeR(), or pass it as auth_token. Remote servers, SSH and headless machines walks through it.
In the organization workspace, only admins can create keys. A member who clicks Create API key sees a dialog listing the organization’s admins to contact.
The key list¶
| Column | Meaning |
|---|---|
| Owner | The member who owns the key (shown to organization admins) |
| Name | The key name |
| Key ID | The key’s prefix and last four characters. It identifies the key but cannot be used as a key. |
| Status | Active or Disabled |
| Jobs, Clusters | Running and completed jobs submitted with the key, and their clusters, including deleted jobs |
| Quota | The key’s cluster limit, or Unlimited |
| Created | The creation date |
The Active filter shows active keys only; All also shows disabled keys. The Sort menu orders keys by date created, name, clusters used, jobs run or quota.
Rename a key or change its quota¶
Click the edit icon next to the name or the quota, change the values and click Save Changes. Leave the quota empty for no per-key limit. In your personal workspace you can edit your own keys. In the organization workspace, only admins can edit keys, and they can edit any organization key.
Disable a key¶
Click Disable and confirm. The key stops working at once: uploads and job submissions that use it are rejected with the error code TOKEN_INACTIVE (an AuthenticationError in Python), and it can no longer fetch the results of private or organization reports. Jobs that are already running still finish; fetch their results with another valid key.
Disabling is permanent. Keys cannot be re-enabled, and they cannot be deleted: disabled keys stay in the list under All as a record. Members can disable their own organization keys; admins can disable any organization key.
The “CyteType CLI” key¶
Browser sign-in (cytetype setup or SetupCyteTypeR()) does not always create a new key. It hands out your active personal key named “CyteType CLI”, including its secret, and creates that key only when you have no active one. So:
every computer you sign in from this way shares one key, and each browser sign-in returns its secret again;
disabling the “CyteType CLI” key here signs all of those computers out, and the next browser sign-in creates a new one (Switch accounts or servers explains how to sign in again after a key was rejected).
For a computer or pipeline that should have a key of its own, create one on this page instead (Remote servers, SSH and headless machines).
cytetype logout and LogoutCyteTypeR() only delete the saved copy on that computer. To stop a key from working anywhere, disable it here.
Account¶
Open the Account page from your email address at the bottom of the sidebar, or at https://cytetype.nygen.io/account. It shows the selected workspace:
Profile: the email address of your account.
Workspace: the workspace name, your role, the license type and, for an organization, the license end date (“No end date” for licenses without one).
Usage and limits:
Personal workspace: the jobs remaining in the last 24 hours, 7 days and 30 days, with how many of each you have used, and the total clusters and datasets you have annotated.
Organization workspace: the clusters annotated in the current license period, the cluster limit, the datasets processed and the clusters remaining.
Appearance: System, Light or Dark.
Support and resources: Contact support (an email to contact@nygen.io), the documentation on GitHub and, in the personal workspace, a link to book a meeting when one is available.
Session: Sign out of this browser.
Usage limits and quotas explains what counts toward each number.
Organization roles¶
Organization members are either admins or members. Admin rights cover API keys; they give no extra access to reports.
| Action | Member | Admin |
|---|---|---|
| Manage their own reports (rename, visibility, share, transfer, archive, delete) | Yes | Yes |
| Open other members’ Organization and Public reports | Yes | Yes |
| Open other members’ private reports | Only if shared with them | Only if shared with them |
| Create organization API keys | No | Yes, for themselves or any active member |
| See organization API keys | Their own | All, with owner and usage |
| Rename keys and change quotas | No | Any organization key |
| Disable keys | Their own | Any organization key |
Admins cannot see members’ personal workspaces (personal reports and personal keys) or their Chat conversations, which are private to each user.
The dashboard has no controls for organization membership or roles. A new account whose email domain belongs to an organization with an active license joins it as a member at its first sign-in. To change admins or license settings, contact contact@nygen.io.
See also¶
Visibility and sharing: what each visibility level and an email share allow.
Usage limits and quotas: what counts toward the numbers on the Account page.
Sign in and API keys: save a key from the API keys page on another computer.