Details
-
Type:
Task
-
Status: To-Do (View Workflow)
-
Priority:
Major
-
Resolution: Unresolved
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:4
-
Epic Link:
-
Sprint:Summer 3, Summer 4, Summer 5
Description
To gain a high level understanding of RadViz, go through the Seurat guided clustering tutorial of PBMC 3K dataset and apply RadViz to the dataset. Goal is to understand the thought process of choosing anchors for a meaningful visualizations, the use of color and other dimensions for further pattern recognition and discern the value of RadViz in single cell data.
Seurat Guided Clustering Tutorial: https://satijalab.org/seurat/articles/pbmc3k_tutorial
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description | To gain a high level understanding of RadViz, go through the Seurat guided clustering tutorial of PBMC 3K dataset and apply RadViz to the dataset. Goal is to understand the thought process of choosing anchors for a meaningful visualizations, the use of color and other dimensions for further pattern recognition and discern the value of RadViz in single cell data. |
To gain a high level understanding of RadViz, go through the Seurat guided clustering tutorial of PBMC 3K dataset and apply RadViz to the dataset. Goal is to understand the thought process of choosing anchors for a meaningful visualizations, the use of color and other dimensions for further pattern recognition and discern the value of RadViz in single cell data.
Seurat Guided Clustering Tutorial: https://satijalab.org/seurat/articles/pbmc3k_tutorial |
| Epic Link | IGBF-3765 [ 22984 ] |
| Sprint | Summer 3 [ 197 ] | Summer 3, Summer 4 [ 197, 198 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Sprint | Summer 3, Summer 4 [ 197, 198 ] | Summer 3, Summer 4, Summer 5 [ 197, 198, 199 ] |
| Rank | Ranked higher |
| Sprint | Summer 3, Summer 4, Summer 5 [ 197, 198, 199 ] | Summer 3, Summer 4, Summer 5, Summer 6 [ 197, 198, 199, 200 ] |
| Rank | Ranked higher |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Summer 3, Summer 4, Summer 5, Summer 6 [ 197, 198, 199, 200 ] | Summer 3, Summer 4, Summer 5 [ 197, 198, 199 ] |
Moving to backlog as this work does not seem feasible at this time.
| Assignee | Karthik Raveendran [ karthik ] |
Details of the dataset: https://www.10xgenomics.com/datasets/3-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0
The output files that is being used for this task is Gene/cell matrix (filtered). There are 3 files in hg19 folder in the downloaded zip file, barcodes.tsv, genes.tsv and matrix.mtx. barcodes.tsv contains the barcodes of individual samples/cells. genes.tsv has the Ensembl ID of each identified gene and its common name. matrix.mtx has the UMI counts of each gene in a sample/cell. matrix.mtx uses the row numbers of the other two .tsv files as unique ids for sample/cell and gene. So the first column is row ids from barcodes.tsv, second column is row ids from genes.tsv and third column is UMI counts.
Currently, the task is to convert this dataset to a format suitable for RadViz where columns are sample/cell barcodes and each row will have the UMI counts for each gene/cell.