Bioinformatics Analysis Pipelines: PCA, WGCNA, and Network Centrality Scripts

Four Jupyter Notebooks for bioinformatics analysis, including scripts for PCA diagnostics, Reactome pathway enrichment, WGCNA module analysis, and graph-based topological centrality. The 1.5 MB archive was authored by Costas Bampos and last updated on April 15, 2026. It is shared under a CC-BY-4.0 license on the figshare platform.

Use Cases

• Perform PCA diagnostics and loadings analysis based on the SVA_Diagnostics_and_PCA_Loadings.ipynb script
• Conduct variance-driven functional enrichment of Reactome pathways based on the PCA_Variance_Driven_Reactome_Enrichment.ipynb script
• Identify and annotate co-expression modules using WGCNA based on the WGCNA_Module_Functional_Enrichment.ipynb script
• Calculate topological centrality measures on Minimum Spanning Trees (MST) based on the igraph_MST_Topological_Centrality.ipynb script

Strengths

• Contains four distinct, named analysis scripts (SVA_Diagnostics_and_PCA_Loadings.ipynb, PCA_Variance_Driven_Reactome_Enrichment.ipynb, WGCNA_Module_Functional_Enrichment.ipynb, igraph_MST_Topological_Centrality.ipynb).
• Shared under a permissive CC-BY-4.0 license, allowing for reuse and modification.
• Small file size of 1.5 MB facilitates quick download and inspection.

Limitations

• Row count and column-level documentation are absent; field semantics must be inferred after download.
• The description metadata is limited to script names; actual data quality and dependencies require manual inspection.

Provenance

Source

Costas Bampos via figshare

Collection Method

Archive of custom analysis scripts, likely created for a specific research project.

Freshness

Last updated 2026-04-15 17:46:43; freshness should be verified.