[Merge on next release] Document how to install cellxgene prepare (#889)

* Document how to install cellxgene prepare

after pr #887 merged

* formatting

* remove reference to cellxgene[louvain]
This commit is contained in:
Charlotte Weaver
2019-09-13 18:15:06 -07:00
committed by Bruce Martin
parent 84c815cc04
commit 0f520f2fd4
3 changed files with 26 additions and 23 deletions
+11 -3
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@@ -14,6 +14,14 @@ description: Data
`cellxgene prepare` is not meant as a way to formally process or analyze your data. It's simply a utility for quickly wrangling your data into cellxgene-compatible format and computing a "vanilla" embedding so you can try out `cellxgene` and get a general sense of a dataset.
#### How do I install `cellxgene prepare`?
The `cellxgene prepare` command is an optional install that you can install alongside `cellxgene launch` by running
```
pip install cellxgene[prepare]
```
#### What input formats does it accept?
Currently, we accept `h5ad` and `loom` files, as well as `10x` directories, and are hoping to accept more formats in the future.
@@ -52,9 +60,9 @@ Let's look at what `prepare` is doing to our data, and how each step relates to
# Example datasets to use with cellxgene
**To download and use these datasets, run:**
`curl -O [URL]`
**To download and use these datasets, run:**
`curl -O [URL]`
`unzip [filename.zip]`
`cellxgene launch [filename.h5ad] --open`