This repository contains the code used for preprocessing transcriptomic files used for Brain Intergrative Transcriptome database (BITHub)
| Dataset | Raw Files | Formatted file |
|---|---|---|
| BrainSpan | columns_metadata.csv rows_metadata.csv expression_matrix.csv |
BrainSpan-metadata.csv BrainSpan-exp.csv |
| BrainSeq | rse_gene_unfiltered.Rdata methprop_pd.Rdata |
BrainSeq-metadata.csv BrainSeq-exp |
| GTEx | GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_tpm.gct.gz |
GTEx-metadata.csv GTEx-exp.csv |
| PsychEncode | Job-154061626746631166818172835.csv DER-24_Cell_fractions_Normalized.xlsx DER-01_PEC_Gene_expression_matrix_TPM.txt |
PsychEncode-metadata.csv PsychEncode-exp.csv |
| DataSet | Raw Files | Formatted files |
|---|---|---|
| Velmesshav et al | ||
| Human Cell Atlas |
All scripts associated with preprocessing files for BITHub are in the preprocessing folder
- git clone https://github.com/WalshKieran/Integration.git
- git checkout datalake
- See very top of Integration/resources/css/style2.js
- Host it locally somehow (e.g. "web server for chrome" > choose folder > ../Integration i.e. root git folder)
- Navigate to http://localhost:8887/site.html (edited)
- Rerun all code and generate with updated pcw values
- Upload data to website
- Move data to RNA
- Update figures for BIThub
- Rerun variance parition
- Write manual and help book for analysis - IN PROGRESS