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-# 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
+# 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](https://drive.google.com/drive/folders/1V1I6pUEiTr2J5Ixma6nM69cd_u1aqiFp?usp=drive_link).
+
+### 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 Series matrix](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25507/matrix/)
+* Schizophrenia dataset - [GSE27383 Series matrix](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE27nnn/GSE27383/matrix/)
+* Depression dataset - [GSE98793 Series matrix](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`
+    * [accession](https://drive.google.com/file/d/1sxfsygRn_wWUaImALhn2uRDrz7WtVQMc/view?usp=drive_link)
+    * [accession2](https://drive.google.com/file/d/1sxfsygRn_wWUaImALhn2uRDrz7WtVQMc/view?usp=drive_link)
+    * [labels](https://drive.google.com/file/d/1QEc0fb7gSLfYwWoTYUyxv_V08myP4nZf/view?usp=drive_link)
+    * Schizophrenia dataset - [GSE80417 Raw Betas](https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE80417&format=file&file=GSE80417%5FrawBetas%2Ecsv%2Egz)
+
+
+* `Methylation_Labeling.ipynb`
+    * [labels](https://drive.google.com/file/d/1QEc0fb7gSLfYwWoTYUyxv_V08myP4nZf/view?usp=drive_link)
+
+
+`differential_methylation_analysis.Rmd`
+
+In order to run the analysis, please download following datasets from GEO database:
+
+* Autism dataset - [GSE109905](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109905/matrix/)
+* Schizophrenia dataset - [GSE80417](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE80nnn/GSE80417/matrix/)
+* Depression dataset - [GSE113725](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE201nnn/GSE201016/matrix/)
+
+
+#### 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](https://drive.google.com/drive/folders/19xE-Op_HhuKsD_RzS7DQ4XFe3gN7WDv6?usp=drive_link)
+    * `/rna-seq` folder for `rnaseq_ml.ipynb` 
+    * `/dna-methylation` folder for `methylation_ml.ipynb`
+
+#### Annotation
+
+`Methylation_Postprocessing.ipynb`
+
+The following files are declared in the notebook's DMP part as df_mdd, df_asd and df_scz:
+* [Depression DMPs](https://drive.google.com/file/d/1-fjNNhFld2ljCBb99UfjbD3NT4YL5VV2/view?usp=drive_link)
+* [Autism DMPS](https://drive.google.com/file/d/1tdVfNiz2Zo3TiH7eaqhDixAcnvmKmoW3/view?usp=drive_link)
+* [Schizophrenia DMPs](https://drive.google.com/file/d/1t1HFzL-MkvLZIGYYLvGhW0C-_JuZglpO/view?usp=drive_link)
+
+The following files are declared in the notebook's GSEA part as mdd, asd and scz:
+* [Depression GSEA](https://drive.google.com/file/d/1-ixarw_W3SKAgMxzlk6Kya_3SWNpDQQc/view?usp=drive_link)
+* [Autism GSEA](https://drive.google.com/file/d/1jQhpZ2XtwpgMXk6leIqdl8YzMAjtVGa3/view?usp=drive_link)
+* [Schizophrenia GSEA](https://drive.google.com/file/d/1O7bcGj97wlLpUwaV_vFNfMfhsTv-0h68/view?usp=drive_link)
+
+`annotation_gsea.ipynb`
+* [Depression dataset](https://drive.google.com/file/d/16AwrCi4ncI51pnR8NItBZdvZRNY4xcgZ/view?usp=drive_link)
+* [Schizophrenia dataset](https://drive.google.com/file/d/1_BYZnRuJznhfDuCA8i18p0g7fyKiyNrL/view?usp=drive_link)
+* [Autism dataset](https://drive.google.com/file/d/1PSrGnP5tZEJ4r3P2f948WjxX67fHJJH5/view?usp=drive_link)