GeoTcgaData

GeoTcgaData processes RNA-seq, DNA Methylation, SNP, and Copy number variation data from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) into formats suitable for bioinformatics analysis.

Key Features:

• TCGA Data Processing: Converts TCGA data downloaded via the gdc tool into analysis-ready formats.
• GEO Data Processing: Handles various data types from the Gene Expression Omnibus repository.
• Multi-omics Support: Processes RNA-seq, DNA Methylation, SNP, and Copy number variation data.

Scientific Applications:

• Cancer Genomics Analysis: Enables downstream bioinformatics analysis of TCGA cancer genomic datasets.
• Gene Expression Studies: Facilitates processing of GEO-hosted transcriptomic and epigenomic data for research.

Methodology:

The package implements data processing methods in R to transform raw GEO and TCGA data into formats suitable for bioinformatics analysis.