Comments (4)
grst
commented on July 18, 2024
In GitLab by @grst on Mar 13, 2020, 11:56
changed the description
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grst
commented on July 18, 2024
In GitLab by @szabogtamas on Mar 26, 2020, 15:48
This package is also very nice (btw, the guy is Hungarian). They started last summer (at least with GitHub), so it is out there quite long ago. Surprising that they did not publish it in a paper.
The upsetplots look especially nice - we might also consider implementing.
Still, it is a puzzle, why it is not advertised more.
Where I think we have an advantage is the clonotype definition. Their package uses 10x definition as is, and that can become confusing if there are many double-chain cells.
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grst
commented on July 18, 2024
In GitLab by @grst on Mar 26, 2020, 18:40
I also like the upset plots. I added a note to the public/private epitope issue (#27)
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grst
commented on July 18, 2024
In GitLab by @grst on Mar 30, 2020, 15:19
closed
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Related Issues (20)
- tl.define_clonotypes within_group parameter returns ValueError HOT 1
- Integrate TCRdist3 HOT 5
- Retrieving specific portions of the Immune Receptor beyond the junction (or CDR3). HOT 2
- ir_dist alignment stuck HOT 4
- IEDB database cdr3_aa stored as junction_aa HOT 10
- Unclear default value for the Hamming Distance cut-off HOT 1
- Dandelion interoperability
- Where has UMI count for AIR chains gone? HOT 1
- Large dataset tutorial
- Make sure axes of nextwork plots don't have any ticks
- Add the Morisita-Horn index for repertoire overlap similarity scores HOT 1
- Sorting logic in `index_chains()` HOT 3
- Community tutorial page
- ir.tl.ir_query fails with error 'ValueError: max_workers must be greater than 0' HOT 1
- ir.tl.clonotype_modularity - ValueError: Length of values does not match length of index HOT 2
- "read_10x_vdj" not loading data properly HOT 2
- clone definition purely using CDR3 sequence HOT 1
- Optimize TCRdist metric HOT 1
- When running 'ir.tl.define_clonotypes' on MacOS14.4.1, I've got an Error:module 'os' has no attribute 'sched_getaffinity' HOT 2
- TypeError: join() got an unexpected keyword argument 'validate' HOT 9
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