scirpy

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scverse datastructure for AIRR data

41

Now that scirpy is part of scverse, we could think of an improved data structure for scAIRR data. See also the discussion at https://github.com/theislab/scanpy/issues/1387. The challenge with scAIRR data is...

grst

Implementing the changes suggested in #327. Close #327 Close #184 Requires * pre-release version of awkward array * Anndata installed from the `val_shape` branch --- **TODO** - [ ] store...

grst

spatial airr data

6

### Description of feature Apparently this is a thing now (e.g. 10x spatial transcriptomics + mixcr, e.g. in [this paper](https://www.sciencedirect.com/science/article/pii/S1074761322000814?via%3Dihub)). @giovp is there anything we need to do to leverage...

grst

Speed up ir_dist

2

Parasail is highly optimized - but it is invoked for every sequence individually from Python which creates a bottleneck. We could solve this issue by integrating with external tools that...

grst

Consistent typing in adata.obs

3

* Most columns added to `adata.obs` should probably be well-defined categoricals * Booleans should be booleans / or categoricals, and not strings * `nan` should be `nan` and not `"nan"`....

grst

Add more epitope databases to `datasets`

4

List adapted from #54. - [ ] The [MAIT reference database](http://www.cbs.dtu.dk/services/MAIT_Match/MAIT_DB_update.php) with invariant CDR3 - [ ] huARdb https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab857/6381136?rss=1 - [ ] McPAS-TCR - [ ] PIRD - [ ]...

grst

airr validation fails when converting demo dataset to_airr_cells

1

### Description of the bug Can't convert demo dataset `to_airr_cells` because of AIRR validation error. ### Minimal reproducible example ```python import scirpy as ir adata = ir.datasets.wu2020_3k() ir.io.to_airr_cells(adata) ``` ###...

grst

scirpy.tl.chain_qc() -- KeyError: 'has_ir'

1

### Description of the bug Hi! I am a first-time user and am having issues getting started with a Scirpy workflow on my dataset. I prepare and preprocess my AnnData...

brian-shim

improve docs build system

4

*Current list of stuff to solve*: - [x] build an overview page of available versions (see also #267) - [ ] move docs to separate repo to keep footprint small...

grst

Why `clonotype_imbalance` is deprecated?

5

Hi @grst, I was wondering why `clonotype_imbalance` is deprecated because of `clonotype_modularity`? `clonotype_imbalance` seems to me still a very useful tool if one wants to compare how the clonal compositions...

naity2