README in progress

README.md

-# DSLS-project
\ No newline at end of file
+# DSLS Project
+## Shared genetic traits in psychiatric disorders
+
+In the project we analyze shared genetic traits between three psychiatric diseases, namely autism, depression and schizophrenia using publicly available RNA-Seq and DNA Methylation datasets.
+
+This repository contains the notebooks with conducted analyses of RNA-Seq and DNA Methylation datasets.
+
+All data necessary to run the notebooks can be downloaded from GEO database and this [link](TODO)
+
+### Statistical analysis
+
+#### Differential Expression Analysis (limma)
+
+`differential_expression_analysis.Rmd`
+
+In order to run the analysis, please download following datasets from GEO database:
+* Autism dataset - [GSE25507](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25507/matrix/)
+* Schizophrenia dataset - [GSE27383](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27383/matrix/)
+* Depression dataset - [GSE98793](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE98nnn/GSE98793/matrix/)
+* Affymetrix chip annotation file - [Platform GPL570](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?mode=raw&is_datatable=true&acc=GPL570&id=55999&db=GeoDb_blob143)
+
+#### Differential Methylation Analysis (ChAMP)
+
+##### Preprocessing
+
+* `GSE80417_Preprocessing.ipynb`
+* `Methylation_Labeling.ipynb`
+
+`differential_methylation_analysis.Rmd`
+
+In order to run the analysis, please download following datasets from GEO database:
+
+TODO
+
+### Machine Learning
+
+Following notebooks contain code for multiclass classification based on RNA-Seq and DNA Methylation data:
+
+* `rnaseq_ml.ipynb` [RNA-Seq]
+* `methylation_ml.ipynb` [DNA Methylation]
+
+In order to run the notebooks, choose one of the two options:
+
+* Run `differential_expression_analysis.Rmd` and `differential_methylation_analysis.Rmd` in order to generate necessary input data
+* (recommended) Download the already generated input data from this [link](TODO)
+
+### Annotation
+
+`Methylation_Postprocessing.ipynb`
+
+TODO
+
+`annotation_gsea.ipynb`
+
+TODO