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README.md

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+# Brain region specific gene regulation after treatment with glucocorticoids
+
+![<img src="./06_Shiny/www/mousejavi_reversebrain.png" width="150"/>](./06_Shiny/www/mousejavi_reversebrain.png) TODO: General text about project, similar to paper abstract.
+
+## 1. Dataset
+
+### 1.1 Experimental setup
+
+TODO: add data overview from slides
+
+### 1.2 Data availability
+
+TODO: add here link to Shiny App where data can be downloaded
+
+## 2. Data analysis
+
+### 2.1 Differential gene expression analysis
+
+Differential gene expression (DE) analysis between mice treated with a vehicle and mice treated with dexamethasone was performed with DESeq2 [cite?] in R. Analysis scripts for the DE analysis can be found in the folder [01_DiffExp](01_DiffExp/).
+
+### 2.2 Differential network analysis
+
+Differential expression networks were calculated with KiMONo [cite?] and DiffGRN [cite?]. As a prior for the network analysis, we used [Funcoup](https://funcoup5.scilifelab.se/search/) which includes functional associations between genes and their respective proteins from various evidence types. Scripts that were used to calculate the expression networks on control and DEX treated samples respectively, can be found in the folder [02_CoExp_Kimono](02_CoExp_Kimono/). 
+
+During the post-processing of the networks inferred by KiMONo, we filtered out interactions with beta or r-squared values below a certain threshold and inferred a *differential gene expression network* for each brain region in our dataset using the DiffGRN [cite?] approach. Scripts used for the post-processing can be found in the folder [03_CoExp_Analysis](03_CoExp_Analysis/).
+
+## 3. Manuscript plots
+
+The plots in our manuscript [link?] were generated with the scripts in the folder (04_PlotsManuscript)[04_PlotsManuscript/].
+
+