From a6d2a2e1196c6766ef57978328708ad14212ab1b Mon Sep 17 00:00:00 2001 From: Justin Kiggins Date: Mon, 28 Jan 2019 10:00:29 -0800 Subject: [PATCH] updates link to scanpy recipe docs. fixes #564 (#565) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 9c7c5853..d45ae70e 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ To prepare from an existing `.h5ad` file use cellxgene prepare dataset.h5ad --output=dataset-processed.h5ad ``` -This will load the input data, perform PCA and nearest neighbor calculations, compute `umap` and `tsne` layouts and `louvain` cluster assignments, and save the results in a new file called `dataset-processed.h5ad` that can be loaded using `cellxgene launch`. Data can be loaded from several formats, including `.h5ad` `.loom` and a `10-Genomics-formatted` `mtx` directory. Several options are available, including running one of the preprocessing `recipes` included with `scanpy`, which include steps like cell filtering and gene selection. To learn more about the `recipes` please see the `scanpy` [documentation](https://github.com/theislab/scanpy/blob/master/scanpy/preprocessing/recipes.py). +This will load the input data, perform PCA and nearest neighbor calculations, compute `umap` and `tsne` layouts and `louvain` cluster assignments, and save the results in a new file called `dataset-processed.h5ad` that can be loaded using `cellxgene launch`. Data can be loaded from several formats, including `.h5ad` `.loom` and a `10-Genomics-formatted` `mtx` directory. Several options are available, including running one of the preprocessing `recipes` included with `scanpy`, which include steps like cell filtering and gene selection. To learn more about the `recipes` please see the `scanpy` [documentation](https://scanpy.readthedocs.io/en/latest/api/index.html#recipes). Depending on the options chosen, `prepare` can take a long time to run (a few minutes for datasets with 10-100k cells, up to an hour or more for datasets with >100k cells). If you want `prepare` to run faster we recommend using the `sparse` option and only computing the layout for `umap`, using a call like this