Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 14:d844935c906c draft

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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 5dada6f76047
comparison
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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>