Merge pull request #1 from slowkow/slowkow-patch-1

update readme

README.md

@@ -1 +1,68 @@
-# airway_allergic_asthma
+Welcome! Here, we present our study of allergic asthma in the human airway.
+
+## Read the paper :mortar_board: 
+
+Please read and cite our original research article:
+
+- CITATION
+
+
+## Explore the data :microscope: 
+<table>
+<tr>
+<td width="33%">
+<a href="https://villani.mgh.harvard.edu/allergy-asthma/app/?ds=AEC_data&gene=MAL&groupby=none">
+<img src="https://user-images.githubusercontent.com/209714/208189301-54950cab-9d7e-46e4-ba95-6f18e0bae550.png"></img>
+</a>
+</td>
+<td>
+<b>Cell Clusters</b>
+
+Metadata variables and gene expression in two-dimensional embeddings.
+
+3 cell lineages:
+
+- Epithelial cells, Mononuclear phagocytes, T cellslls
+
+:point_right: <a href="https://villani.mgh.harvard.edu/allergy-asthma/app/?ds=AEC_data&gene=MAL&groupby=none">View Cell Clusters</a>
+</td>
+</tr>
+<tr>
+<td>
+<a href="https://villani.mgh.harvard.edu/allergy-asthma/gene-contrasts/">
+<img src="https://user-images.githubusercontent.com/209714/208189495-d2c43409-d81e-4e06-86b8-5567ac79dc36.png"></img>
+</a>
+</td>
+<td>
+<b>Gene Contrasts</b>
+
+Differential expression statistics for all genes across:
+
+- 2 contrasts (condition Ag vs Bln, group AA vs AC)
+
+:point_right: <a href="https://villani.mgh.harvard.edu/allergy-asthma/gene-contrasts/">View Gene Contrasts</a>
+</td>
+</tr>
+</table>
+
+
+## Read the source code &#x1F4BB;
+
+This repository includes two folders:
+
+[deg_table/][deg_table]
+- The differentially expressed gene tables.
+
+[figure_scripts/][figure_scripts]
+- The source code for creating the figures that appear in the manuscript.
+
+[deg_table]: https://github.com/villani-lab/airway_allergic_asthma/tree/main/deg_table
+[figure_scripts]: https://github.com/villani-lab/airway_allergic_asthma/tree/main/figure_scripts
+
+
+## Download the data &#x1F4BE;
+
+The raw and processed scRNA-seq gene expression files are available at NCBI GEO
+[GSE193816].
+
+[GSE193816]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193816