Mercurial > repos > iuc > scanpy_normalize
comparison normalize.xml @ 14:d844935c906c 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 18:31:20 +0000 |
| parents | 7b9fafe32c86 |
| children |
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| 13:7b9fafe32c86 | 14:d844935c906c |
|---|---|
| 320 the same total count after normalization. | 320 the same total count after normalization. |
| 321 | 321 |
| 322 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. | 322 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. |
| 323 | 323 |
| 324 More details on the `scanpy documentation | 324 More details on the `scanpy documentation |
| 325 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__ | 325 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.normalize_per_cell.html>`__ |
| 326 | 326 |
| 327 | 327 |
| 328 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) | 328 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) |
| 329 ================================================================================================================== | 329 ================================================================================================================== |
| 330 | 330 |
| 339 - renormalize after filtering | 339 - renormalize after filtering |
| 340 - log transform (if needed) | 340 - log transform (if needed) |
| 341 - scale to unit variance and shift to zero mean | 341 - scale to unit variance and shift to zero mean |
| 342 | 342 |
| 343 More details on the `scanpy documentation | 343 More details on the `scanpy documentation |
| 344 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__ | 344 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_zheng17.html>`__ |
| 345 | 345 |
| 346 | 346 |
| 347 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) | 347 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) |
| 348 ============================================================================== | 348 ============================================================================== |
| 349 | 349 |
| 350 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. | 350 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. |
| 351 | 351 |
| 352 More details on the `scanpy documentation | 352 More details on the `scanpy documentation |
| 353 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__ | 353 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_weinreb17.html>`__ |
| 354 | 354 |
| 355 | 355 |
| 356 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) | 356 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) |
| 357 ========================================================================== | 357 ========================================================================== |
| 358 | 358 |
| 359 This uses a particular preprocessing. | 359 This uses a particular preprocessing. |
| 360 | 360 |
| 361 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. | 361 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. |
| 362 | 362 |
| 363 More details on the `scanpy documentation | 363 More details on the `scanpy documentation |
| 364 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__ | 364 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.recipe_seurat.html>`__ |
| 365 | 365 |
| 366 | 366 |
| 367 Markov Affinity-based Graph Imputation of Cells (MAGIC) as of Van Dijk D et al. (2018) (`external.pp.magic`) | 367 Markov Affinity-based Graph Imputation of Cells (MAGIC) as of Van Dijk D et al. (2018) (`external.pp.magic`) |
| 368 ============================================================================================================ | 368 ============================================================================================================ |
| 369 | 369 |
| 373 | 373 |
| 374 - Firstly, we use the adaptive kernel described in Moon et al, (2019) for improved stability. | 374 - Firstly, we use the adaptive kernel described in Moon et al, (2019) for improved stability. |
| 375 - Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements. | 375 - Secondly, data diffusion is applied in the PCA space, rather than the data space, for speed and memory improvements. |
| 376 | 376 |
| 377 More details on the `scanpy documentation | 377 More details on the `scanpy documentation |
| 378 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.external.pp.magic.html>`__ | 378 <https://scanpy.readthedocs.io/en/stable/api/scanpy.external.pp.magic.html>`__ |
| 379 | 379 |
| 380 ]]></help> | 380 ]]></help> |
| 381 <expand macro="citations"/> | 381 <expand macro="citations"/> |
| 382 </tool> | 382 </tool> |