Mercurial > repos > iuc > scanpy_remove_confounders
comparison remove_confounders.xml @ 5:e5fa012d8d93 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
| author | iuc |
|---|---|
| date | Mon, 10 Feb 2020 10:17:47 +0000 |
| parents | 5a97db811365 |
| children | c0fab89336d1 |
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| 4:e566e361a23e | 5:e5fa012d8d93 |
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| 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> |