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  1. IGB
  2. IGBF-4354

Add links to 10X Genomics dataset pages to the single-cell QL

    Details

    • Type: Task
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Done
    • Affects Version/s: None
    • Fix Version/s: None
    • Labels:
      None

      Description

      Karthik Raveendran has made a really nice, curated Quickload that IGB users can use to load and explore alignments from several single-cell RNA-Seq "demonstration" datasets provided by 10X Genomics.

      To add his Quickload to IGB, you can enter this URL as a new Quickload using the Settings > Data Sources tab as usual:

      And so the code for his Quickoad is in this repository:

      Note that a "file" tag in a Quickload repository can provide a Web address for each dataset. If provided, then IGB will display a linkout icon in the Available Data Sources menu.

      Also, 10X Genomics provides a very nice, no login required Web site for each of its datasets, including the ones Karthik included in his Quickload. To make this single-cell demonstration Quickload 1000 times more useful, let's add those URLs to the Quickload File tages so that users can very quickly and easily find out the full range of information about those datasets.

      The attribute that is needed is "url" and you can use it to specify the location for the dataset's page.

      I hope somebody can do this ASAP because I am preparing a lecture where I'm going to show my students how to browse these datasets in IGB!

      SCOPE CHANGE: Per Dr. Loraine's comment on 11/12, I will now be curating the track labels as part of this ticket, too.

        Attachments

          Activity

          ann.loraine Ann Loraine created issue -
          ann.loraine Ann Loraine made changes -
          Field Original Value New Value
          Epic Link IGBF-1765 [ 17855 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Paige Kulzer [ pkulzer ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
          ann.loraine Ann Loraine made changes -
          Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
          ann.loraine Ann Loraine made changes -
          Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
          ann.loraine Ann Loraine made changes -
          Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
          ann.loraine Ann Loraine made changes -
          Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status To-Do [ 10305 ] In Progress [ 3 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Description [~karthik] has made a really nice, curated Quickload that IGB users can use to load and explore alignments from several single-cell RNA-Seq "demonstration" datasets provided by 10X Genomics.

          To add his Quickload to IGB, you can enter this URL as a new Quickload using the Settings > Data Sources tab as usual:

          * https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/raw/main/

          And so the code for his Quickoad is in this repository:

          * https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics

          Note that a "file" tag in a Quickload repository can provide a Web address for each dataset. If provided, then IGB will display a linkout icon in the Available Data Sources menu.

          Also, 10X Genomics provides a very nice, no login required Web site for each of its datasets, including the ones Karthik included in his Quickload. To make this single-cell demonstration Quickload 1000 times more useful, let's add those URLs to the Quickload File tages so that users can very quickly and easily find out the full range of information about those datasets.

          The attribute that is needed is "url" and you can use it to specify the location for the dataset's page.

          I hope somebody can do this ASAP because I am preparing a lecture where I'm going to show my students how to browse these datasets in IGB!

          [~karthik] has made a really nice, curated Quickload that IGB users can use to load and explore alignments from several single-cell RNA-Seq "demonstration" datasets provided by 10X Genomics.

          To add his Quickload to IGB, you can enter this URL as a new Quickload using the Settings > Data Sources tab as usual:

          * https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/raw/main/

          And so the code for his Quickoad is in this repository:

          * https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics

          Note that a "file" tag in a Quickload repository can provide a Web address for each dataset. If provided, then IGB will display a linkout icon in the Available Data Sources menu.

          Also, 10X Genomics provides a very nice, no login required Web site for each of its datasets, including the ones Karthik included in his Quickload. To make this single-cell demonstration Quickload 1000 times more useful, let's add those URLs to the Quickload File tages so that users can very quickly and easily find out the full range of information about those datasets.

          The attribute that is needed is "url" and you can use it to specify the location for the dataset's page.

          I hope somebody can do this ASAP because I am preparing a lecture where I'm going to show my students how to browse these datasets in IGB!

          *SCOPE CHANGE:* Per Dr. Loraine's comment on 11/12, I will now be curating the track labels as part of this ticket, too.
          pkulzer Paige Kulzer (Inactive) made changes -
          Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
          ann.loraine Ann Loraine made changes -
          Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
          ann.loraine Ann Loraine made changes -
          Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]
          ann.loraine Ann Loraine made changes -
          Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Paige Kulzer [ pkulzer ] Karthik Raveendran [ karthik ]
          nfreese Nowlan Freese made changes -
          Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
          nfreese Nowlan Freese made changes -
          Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
          nfreese Nowlan Freese made changes -
          Assignee Karthik Raveendran [ karthik ] Paige Kulzer [ pkulzer ]
          pkulzer Paige Kulzer (Inactive) made changes -
          Assignee Paige Kulzer [ pkulzer ] Ann Loraine [ aloraine ]
          ann.loraine Ann Loraine made changes -
          Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
          ann.loraine Ann Loraine made changes -
          Resolution Done [ 10000 ]
          Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
          ann.loraine Ann Loraine made changes -
          Assignee Ann Loraine [ aloraine ] Paige Kulzer [ pkulzer ]

            People

            • Assignee:
              pkulzer Paige Kulzer (Inactive)
              Reporter:
              ann.loraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              2 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: