Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-4340

Create python scripts to work with 10xGenomics files

        Details

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

          Description

          The goal of this task is to implement data preparation scripts that transform the input CSV file into a structure optimized for integration with IGB’s single-cell feature modules. Scripts such as:
          1) Color mapper for Loupe Browser barcode grouping files - Map Loupe browser cluster colors to the barcode grouping file
          2) HDF5 barcodes extractor

          These code for scripts will be is housed in https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/src/main/python_for_%20scRNA-seq/

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-4341 Create a scRNA-Seq tutorial

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                karthik Karthik Raveendran created issue -
                karthik Karthik Raveendran made changes -
                Field Original Value New Value
                Epic Link IGBF-3765 [ 22984 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer (Inactive) made changes -
                Link This issue relates to IGBF-4341 [ IGBF-4341 ]
                nfreese Nowlan Freese made changes -
                Sprint Fall 5 [ 228 ] Fall 5, Fall 6 [ 228, 229 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5, Fall 6 [ 228, 229 ] Fall 5, Fall 6, Fall 7 [ 228, 229, 230 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5, Fall 6, Fall 7 [ 228, 229, 230 ] Fall 5, Fall 6, Fall 7, Fall 8 [ 228, 229, 230, 231 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                pkulzer Paige Kulzer (Inactive) made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5, Fall 6, Fall 7, Fall 8 [ 228, 229, 230, 231 ] Fall 5, Fall 6, Fall 7, Fall 8, Fall 9 [ 228, 229, 230, 231, 232 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Sprint Fall 5, Fall 6, Fall 7, Fall 8, Fall 9 [ 228, 229, 230, 231, 232 ] Fall 5, Fall 6, Fall 7, Fall 8 [ 228, 229, 230, 231 ]
                nfreese Nowlan Freese made changes -
                Sprint Fall 5, Fall 6, Fall 7, Fall 8 [ 228, 229, 230, 231 ] Fall 5, Fall 6, Fall 7, Fall 8, Spring 1 [ 228, 229, 230, 231, 233 ]
                nfreese Nowlan Freese made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Sprint Fall 5, Fall 6, Fall 7, Fall 8, Spring 1 [ 228, 229, 230, 231, 233 ] Fall 5, Fall 6, Fall 7, Fall 8 [ 228, 229, 230, 231 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                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 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                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 Karthik Raveendran [ karthik ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    karthik Karthik Raveendran
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: