From b50098c137b565139922c533fa7c284eb413fa6c Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 9 Jan 2020 09:48:25 +0100 Subject: [PATCH] Linking tutorial more prominently in home.md. (#37) * Linking tutorial more prominently in home.md. --- docs_manual/index.rst | 4 ++-- scelvis/static/home.md | 19 ++++++++++++------- 2 files changed, 14 insertions(+), 9 deletions(-) diff --git a/docs_manual/index.rst b/docs_manual/index.rst index 9b3ff03..c04783a 100644 --- a/docs_manual/index.rst +++ b/docs_manual/index.rst @@ -11,9 +11,9 @@ Getting Started --------------- - you can find the **publically available web app** at https://scelvis-demo.bihealth.org. -- to get started with your analysis, follow the :ref:`tutorial_analysis`. +- to get started with your analysis, watch the `Movie `_ or follow the :ref:`tutorial_analysis`. - to learn how to get your own data into SCelVis, read about :ref:`tutorial_input_formats`. -- if you are a bioinformatician and interested in running your own SCelVis server, follow the :ref:`tutorial_cli`. +- if you are a bioinformatician and interested in running your own SCelVis server, read the :ref:`tutorial_cli`. ------------------------ diff --git a/scelvis/static/home.md b/scelvis/static/home.md index 9ff57ec..b2bc30a 100644 --- a/scelvis/static/home.md +++ b/scelvis/static/home.md @@ -1,17 +1,22 @@ -### ScelVis Quickstart +### SCelVis SCelVis is a web app for the visualization and interactive exploration of single-cell transcriptomic data. -**Start by selecting the dataset you want to work with from the `Go To` menu on the top right**: -choose an existing dataset, or upload a new one. +#### Quickstart + +- Start by selecting the dataset you want to work with from the `Go To` menu on the top right: choose an existing dataset, or upload a new one. +- check out our [Documentation](https://scelvis.readthedocs.io/en/latest/index.html), in particular the [Tutorial](https://scelvis.readthedocs.io/en/latest/tutorial_analysis.html), or the movie on our [github page](https://github.com/bihealth/scelvis#Movie) +- some example data to upload: [PBMCs](https://files.figshare.com/18037739/pbmc.h5ad), [human-mouse mix](https://github.com/bihealth/scelvis/raw/master/examples/hgmm_1k.h5ad). + +#### Main user interface ![go to https://github.com/bihealth/scelvis for an animated tutorial](https://raw.githubusercontent.com/bihealth/scelvis/master/scelvis/static/scelvis_screenshot.png) 1. switch between tabs: - * `About`: information about dataset - * `Cell Annotation`: browse cell meta data - * `Gene Expression`: explore gene expression + - `About`: information about dataset + - `Cell Annotation`: browse cell meta data + - `Gene Expression`: explore gene expression 2. select plot type @@ -19,7 +24,7 @@ choose an existing dataset, or upload a new one. 4. choose x- and y-axis of scatter plot (usually embeddings like tSNE or UMAP) -5. perform differential expression analysis between groups of cells selected on the plt +5. open control panel to perform differential expression analysis between groups of cells selected on the scatter plot 6. hover over points on the plot to get more information