phantasusLite

phantasusLite simplifies working with public RNA-seq datasets from GEO by providing helper functions that access a remote HSDS repository containing precomputed gene counts from ARCHS4 and DEE2 projects.

Key Features:

• GEO RNA-seq data access: Provides streamlined access to public RNA-seq datasets from the Gene Expression Omnibus (GEO) repository.
• Remote HSDS repository connection: Connects to a remote HSDS (Highly Scalable Data Service) repository to retrieve precomputed gene count data.
• ARCHS4 and DEE2 integration: Accesses precomputed gene counts from the ARCHS4 and DEE2 projects.
• Helper functions for RNA-seq matrices: Offers utility functions for loading and annotating RNA-seq counts matrices.

Scientific Applications:

• Public RNA-seq data analysis: Enables researchers to utilize preprocessed gene expression data from large-scale public RNA-seq compendia without local computation of read counts.
• Gene expression studies: Facilitates retrieval of annotated counts matrices for downstream differential expression and transcriptomic analysis workflows.

Methodology:

The package extracts helper functions of general interest from the phantasus package and provides access to precomputed gene counts stored in a remote HSDS repository.