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Analyses on TCGA data - Part of bachelor thesis studying DNA methylation valleys in breast cancer

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.ipynb_checkpoints
.ipynb_checkpoints
 
 
GDCdata/TCGA-BRCA
GDCdata/TCGA-BRCA
 
 
datasets
datasets
 
 
metadata
metadata
 
 
plots
plots
 
 
.gitignore
.gitignore
 
 
BigQuery_Practice.ipynb
BigQuery_Practice.ipynb
 
 
Cluster_expression_hormone.ipynb
Cluster_expression_hormone.ipynb
 
 
Cluster_expression_subtype.ipynb
Cluster_expression_subtype.ipynb
 
 
Cluster_meth_hormone.ipynb
Cluster_meth_hormone.ipynb
 
 
Cluster_meth_hormone_wo_unknown.ipynb
Cluster_meth_hormone_wo_unknown.ipynb
 
 
Cluster_meth_subtype.ipynb
Cluster_meth_subtype.ipynb
 
 
Corr_genes_function.ipynb
Corr_genes_function.ipynb
 
 
Correlation_meth_expression.ipynb
Correlation_meth_expression.ipynb
 
 
Extract.RNASeq_data.ipynb
Extract.RNASeq_data.ipynb
 
 
Extract.case_barcode.ipynb
Extract.case_barcode.ipynb
 
 
Extract.gene.ipynb
Extract.gene.ipynb
 
 
Extract.meth_data.ipynb
Extract.meth_data.ipynb
 
 
Extract.probe_id.ipynb
Extract.probe_id.ipynb
 
 
Extract.sample_barcode.ipynb
Extract.sample_barcode.ipynb
 
 
MANIFEST.txt
MANIFEST.txt
 
 
README.md
README.md
 
 
Visualize_expression_hormone.ipynb
Visualize_expression_hormone.ipynb
 
 
Visualize_expression_subtype.ipynb
Visualize_expression_subtype.ipynb
 
 
Visualize_meth_hormone.ipynb
Visualize_meth_hormone.ipynb
 
 
Visualize_meth_subtype.ipynb
Visualize_meth_subtype.ipynb
 
 
Visualize_numbers.ipynb
Visualize_numbers.ipynb
 
 

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Analyses on TCGA data studying DNA methylation valleys in breast cancer

Preliminary results

In preliminary folder, results from prior analyses on WGBS data are stored.
These include positions of DMV signatures that are differentially methylated in triple negative and/or in endocrine resistant tumors; and their associated genes.

Access and query TCGA data on Google BigQuery

Requirements

  • Have a billing enabled Google Cloud Platform (GCP) project
  • In the GCP project, BigQuery API is enabled.
  • Authentication is set up.
  • Python package google-cloud-bigquery is installed. Can be by conda install -c conda-forge google-cloud-bigquery

For detailed instructions: go here

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Analyses on TCGA data - Part of bachelor thesis studying DNA methylation valleys in breast cancer

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transcriptomics oncology epigenomics

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