Mercurial > repos > iuc > scanpy_filter
comparison filter.xml @ 14:d636ce5cde16 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
| author | iuc |
|---|---|
| date | Sat, 18 May 2024 18:29:27 +0000 |
| parents | a03ff8633507 |
| children |
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| 13:277313130da5 | 14:d636ce5cde16 |
|---|---|
| 456 | 456 |
| 457 Only provide one of the optional parameters `min_counts`, `min_genes`, | 457 Only provide one of the optional parameters `min_counts`, `min_genes`, |
| 458 `max_counts`, `max_genes` per call. | 458 `max_counts`, `max_genes` per call. |
| 459 | 459 |
| 460 More details on the `scanpy documentation | 460 More details on the `scanpy documentation |
| 461 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_cells.html>`__ | 461 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_cells.html>`__ |
| 462 | 462 |
| 463 | 463 |
| 464 Filter genes based on number of cells or counts (`pp.filter_genes`) | 464 Filter genes based on number of cells or counts (`pp.filter_genes`) |
| 465 =================================================================== | 465 =================================================================== |
| 466 | 466 |
| 470 | 470 |
| 471 Only provide one of the optional parameters `min_counts`, `min_cells`, | 471 Only provide one of the optional parameters `min_counts`, `min_cells`, |
| 472 `max_counts`, `max_cells` per call. | 472 `max_counts`, `max_cells` per call. |
| 473 | 473 |
| 474 More details on the `scanpy documentation | 474 More details on the `scanpy documentation |
| 475 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_genes.html>`__ | 475 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.filter_genes.html>`__ |
| 476 | 476 |
| 477 | 477 |
| 478 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`) | 478 Filters out genes based on fold change and fraction of genes expressing the gene within and outside the groupby categories (`tl.filter_rank_genes_groups`) |
| 479 ========================================================================================================================================================== | 479 ========================================================================================================================================================== |
| 480 | 480 |
| 481 More details on the `scanpy documentation | 481 More details on the `scanpy documentation |
| 482 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__ | 482 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__ |
| 483 | 483 |
| 484 | 484 |
| 485 Annotate highly variable genes (`pp.highly_variable_genes`) | 485 Annotate highly variable genes (`pp.highly_variable_genes`) |
| 486 =========================================================== | 486 =========================================================== |
| 487 | 487 |
| 492 | 492 |
| 493 Subsample to a fraction of the number of observations (`pp.subsample`) | 493 Subsample to a fraction of the number of observations (`pp.subsample`) |
| 494 ====================================================================== | 494 ====================================================================== |
| 495 | 495 |
| 496 More details on the `scanpy documentation | 496 More details on the `scanpy documentation |
| 497 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.subsample.html>`__ | 497 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.subsample.html>`__ |
| 498 | 498 |
| 499 Downsample counts (`pp.downsample_counts`) | 499 Downsample counts (`pp.downsample_counts`) |
| 500 ========================================== | 500 ========================================== |
| 501 | 501 |
| 502 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This | 502 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This |
| 503 has been implemented by M. D. Luecken. | 503 has been implemented by M. D. Luecken. |
| 504 | 504 |
| 505 More details on the `scanpy documentation | 505 More details on the `scanpy documentation |
| 506 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.downsample_counts.html>`__ | 506 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.downsample_counts.html>`__ |
| 507 | 507 |
| 508 | 508 |
| 509 ]]></help> | 509 ]]></help> |
| 510 <expand macro="citations"/> | 510 <expand macro="citations"/> |
| 511 </tool> | 511 </tool> |