Mercurial > repos > iuc > scanpy_filter
comparison filter.xml @ 5:8b9610ab366a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
| author | iuc |
|---|---|
| date | Mon, 10 Feb 2020 05:29:59 -0500 |
| parents | 0a6de5e65992 |
| children | a97abb8cd15b |
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| 4:a72e9faea895 | 5:8b9610ab366a |
|---|---|
| 405 | 405 |
| 406 Only provide one of the optional parameters `min_counts`, `min_genes`, | 406 Only provide one of the optional parameters `min_counts`, `min_genes`, |
| 407 `max_counts`, `max_genes` per call. | 407 `max_counts`, `max_genes` per call. |
| 408 | 408 |
| 409 More details on the `scanpy documentation | 409 More details on the `scanpy documentation |
| 410 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_cells.html>`__ | 410 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_cells.html>`__ |
| 411 | 411 |
| 412 | 412 |
| 413 Filter genes based on number of cells or counts (`pp.filter_genes`) | 413 Filter genes based on number of cells or counts (`pp.filter_genes`) |
| 414 =================================================================== | 414 =================================================================== |
| 415 | 415 |
| 419 | 419 |
| 420 Only provide one of the optional parameters `min_counts`, `min_cells`, | 420 Only provide one of the optional parameters `min_counts`, `min_cells`, |
| 421 `max_counts`, `max_cells` per call. | 421 `max_counts`, `max_cells` per call. |
| 422 | 422 |
| 423 More details on the `scanpy documentation | 423 More details on the `scanpy documentation |
| 424 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.filter_genes.html>`__ | 424 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.filter_genes.html>`__ |
| 425 | 425 |
| 426 | 426 |
| 427 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`) | 427 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`) |
| 428 ========================================================================================================================================================== | 428 ========================================================================================================================================================== |
| 429 | 429 |
| 430 More details on the `scanpy documentation | 430 More details on the `scanpy documentation |
| 431 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.filter_rank_genes_groups.html>`__ | 431 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.tl.filter_rank_genes_groups.html>`__ |
| 432 | 432 |
| 433 | 433 |
| 434 Annotate highly variable genes (`pp.highly_variable_genes`) | 434 Annotate highly variable genes (`pp.highly_variable_genes`) |
| 435 =========================================================== | 435 =========================================================== |
| 436 | 436 |
| 441 | 441 |
| 442 Subsample to a fraction of the number of observations (`pp.subsample`) | 442 Subsample to a fraction of the number of observations (`pp.subsample`) |
| 443 ====================================================================== | 443 ====================================================================== |
| 444 | 444 |
| 445 More details on the `scanpy documentation | 445 More details on the `scanpy documentation |
| 446 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.subsample.html>`__ | 446 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.subsample.html>`__ |
| 447 | 447 |
| 448 Downsample counts (`pp.downsample_counts`) | 448 Downsample counts (`pp.downsample_counts`) |
| 449 ========================================== | 449 ========================================== |
| 450 | 450 |
| 451 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This | 451 Downsample counts so that each cell has no more than `target_counts`. Cells with fewer counts than `target_counts` are unaffected by this. This |
| 452 has been implemented by M. D. Luecken. | 452 has been implemented by M. D. Luecken. |
| 453 | 453 |
| 454 More details on the `scanpy documentation | 454 More details on the `scanpy documentation |
| 455 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.downsample_counts.html>`__ | 455 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.downsample_counts.html>`__ |
| 456 | 456 |
| 457 | 457 |
| 458 ]]></help> | 458 ]]></help> |
| 459 <expand macro="citations"/> | 459 <expand macro="citations"/> |
| 460 </tool> | 460 </tool> |