README additional info

42a1b49c · vbendikova · b143ed0d · 42a1b49c
Commit 42a1b49c authored 1 year ago by vbendikova
--- a/README.md
+++ b/README.md
 # 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)
+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](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25507/matrix/)
+* Autism dataset - [GSE25507 Series matrix](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/)
+* Schizophrenia dataset - [GSE27383 Series matrix](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/)
+* 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`
-* `Methylation_Labeling.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)
-`differential_methylation_analysis.Rmd`
+    * [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)
-In order to run the analysis, please download following datasets from GEO database:
-TODO
+* `Methylation_Labeling.ipynb`
+    * [labels](https://drive.google.com/file/d/1QEc0fb7gSLfYwWoTYUyxv_V08myP4nZf/view?usp=drive_link)
-### Machine Learning
-Following notebooks contain code for multiclass classification based on RNA-Seq and DNA Methylation data:
+`differential_methylation_analysis.Rmd`
-* `rnaseq_ml.ipynb` [RNA-Seq]
+In order to run the analysis, please download following datasets from GEO database:
-* `methylation_ml.ipynb` [DNA Methylation]
+* Autism dataset - [GSE109905](https://ftp.ncbi.nlm.nih.gov/geo/series/GSE109nnn/GSE109905/matrix/)
-In order to run the notebooks, choose one of the two options:
+* 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/)
-* 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)
+#### Machine Learning
-### Annotation
+Following notebooks contain code for multiclass classification based on RNA-Seq and DNA Methylation data:
-`Methylation_Postprocessing.ipynb`
+* `rnaseq_ml.ipynb` [RNA-Seq]
-TODO
+* `methylation_ml.ipynb` [DNA Methylation]
-`annotation_gsea.ipynb`
+In order to run the notebooks, choose one of the two options:
-TODO
+* 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)