Mercurial > repos > iuc > scanpy_remove_confounders
comparison remove_confounders.xml @ 5:524aa62a6066 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
author | iuc |
---|---|
date | Mon, 10 Feb 2020 05:27:49 -0500 |
parents | 00305dc2dd6f |
children | f2f6c703da06 |
comparison
equal
deleted
inserted
replaced
4:7a6701edcc92 | 5:524aa62a6066 |
---|---|
154 | 154 |
155 Regress out unwanted sources of variation, using simple linear regression. This is | 155 Regress out unwanted sources of variation, using simple linear regression. This is |
156 inspired by Seurat's `regressOut` function in R. | 156 inspired by Seurat's `regressOut` function in R. |
157 | 157 |
158 More details on the `scanpy documentation | 158 More details on the `scanpy documentation |
159 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.regress_out.html>`__ | 159 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.regress_out.html>`__ |
160 | 160 |
161 Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct` | 161 Correct batch effects by matching mutual nearest neighbors, using `pp.mnn_correct` |
162 ================================================================================== | 162 ================================================================================== |
163 | 163 |
164 This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the | 164 This uses the implementation of mnnpy. Depending on do_concatenate, it returns AnnData objects in the |
165 original order containing corrected expression values or a concatenated matrix or AnnData object. | 165 original order containing corrected expression values or a concatenated matrix or AnnData object. |
166 | 166 |
167 Be reminded that it is not advised to use the corrected data matrices for differential expression testing. | 167 Be reminded that it is not advised to use the corrected data matrices for differential expression testing. |
168 | 168 |
169 More details on the `scanpy documentation | 169 More details on the `scanpy documentation |
170 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.api.pp.mnn_correct.html>`__ | 170 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.api.pp.mnn_correct.html>`__ |
171 | 171 |
172 | 172 |
173 Correct batch effects with ComBat function (`pp.combat`) | 173 Correct batch effects with ComBat function (`pp.combat`) |
174 ======================================================== | 174 ======================================================== |
175 | 175 |
176 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat | 176 Corrects for batch effects by fitting linear models, gains statistical power via an EB framework where information is borrowed across genes. This uses the implementation of ComBat |
177 | 177 |
178 More details on the `scanpy documentation | 178 More details on the `scanpy documentation |
179 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.combat.html>`__ | 179 <https://icb-scanpy.readthedocs-hosted.com/en/@version@/api/scanpy.pp.combat.html>`__ |
180 | 180 |
181 | 181 |
182 ]]></help> | 182 ]]></help> |
183 <expand macro="citations"/> | 183 <expand macro="citations"/> |
184 </tool> | 184 </tool> |