diff --git a/README.md b/README.md index 9d4944caf2df208c957a9e60474fa4446cdef902..3d1b2f05283798ef579901982715b503a15242fc 100644 --- a/README.md +++ b/README.md @@ -1 +1,55 @@ -# 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