Mercurial > repos > iuc > scanpy_normalize

comparison normalize.xml @ 5:df4124e38f46 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
author iuc
date Mon, 10 Feb 2020 10:18:25 +0000
parents 288782468dc1
children 51b1da3700c1
comparison
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4:9270b707fb0d 5:df4124e38f46
201 the same total count after normalization. 201 the same total count after normalization.
202 202
203 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING. 203 Similar functions are used, for example, by Seurat, Cell Ranger or SPRING.
204 204
205 More details on the `scanpy documentation 205 More details on the `scanpy documentation
206 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.normalize_per_cell.html>`__ 206 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.normalize_per_cell.html>`__
207 207
208 208
209 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`) 209 Normalization and filtering as of Zheng et al. (2017), the Cell Ranger R Kit of 10x Genomics (`pp.recipe_zheng17`)
210 ================================================================================================================== 210 ==================================================================================================================
211 211
220 - renormalize after filtering 220 - renormalize after filtering
221 - log transform (if needed) 221 - log transform (if needed)
222 - scale to unit variance and shift to zero mean 222 - scale to unit variance and shift to zero mean
223 223
224 More details on the `scanpy documentation 224 More details on the `scanpy documentation
225 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_zheng17.html>`__ 225 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_zheng17.html>`__
226 226
227 227
228 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`) 228 Normalization and filtering as of Weinreb et al (2017) (`pp.recipe_weinreb17`)
229 ============================================================================== 229 ==============================================================================
230 230
231 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. 231 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
232 232
233 More details on the `scanpy documentation 233 More details on the `scanpy documentation
234 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_weinreb17.html>`__ 234 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_weinreb17.html>`__
235 235
236 236
237 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`) 237 Normalization and filtering as of Seurat et al (2015) (`pp.recipe_seurat`)
238 ========================================================================== 238 ==========================================================================
239 239
240 This uses a particular preprocessing. 240 This uses a particular preprocessing.
241 241
242 Expects non-logarithmized data. If using logarithmized data, pass `log=False`. 242 Expects non-logarithmized data. If using logarithmized data, pass `log=False`.
243 243
244 More details on the `scanpy documentation 244 More details on the `scanpy documentation
245 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.recipe_seurat.html>`__ 245 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.recipe_seurat.html>`__
246 246
247 ]]></help> 247 ]]></help>
248 <expand macro="citations"/> 248 <expand macro="citations"/>
249 </tool> 249 </tool>