Mercurial > repos > iuc > scater_normalize
comparison README.md @ 1:b32ae8dfa72b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
| author | iuc |
|---|---|
| date | Tue, 03 Sep 2019 14:23:23 -0400 |
| parents | 0cb9a5f830fc |
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| 0:0cb9a5f830fc | 1:b32ae8dfa72b |
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| 17 5. Normalise data with `scater-normalize`. | 17 5. Normalise data with `scater-normalize`. |
| 18 6. Investigate other confounding factors.\ | 18 6. Investigate other confounding factors.\ |
| 19 Plot the data (using PCA) and display various annotated properties of the cells using `scater-plot-pca`. | 19 Plot the data (using PCA) and display various annotated properties of the cells using `scater-plot-pca`. |
| 20 | 20 |
| 21 ## Command-line usage | 21 ## Command-line usage |
| 22 | |
| 23 The scripts require the installation of scater and few other R/BioConductor packages. An easy way to install them is to create a [conda](https://conda.io/) environment using the `environment.yml` file distributed together with these wrappers: | |
| 24 | |
| 25 ``` | |
| 26 conda env create -f environment.yml | |
| 27 conda activate scater | |
| 28 ``` | |
| 22 | 29 |
| 23 For help with any of the following scripts, run: | 30 For help with any of the following scripts, run: |
| 24 `<script-name> --help` | 31 `<script-name> --help` |
| 25 | 32 |
| 26 --- | 33 --- |