Crate bixverse_methods 

Bulk omics methods on top of bixverse-core: gene set enrichment, graphs and community detection, ontologies, matrix factorisation, co-expression and (feature dge) the edgeR / limma differential expression chain.

Feature flags

• dge — The negative binomial differential expression methods built on edge-rs: the edgeR quasi-likelihood chain and the limma linear model chain.
• large-test — Slow but asserting tests. Run in release.
• large_scale_diagnostics — Unasserted diagnostic sweeps that print tables for a human to read.

Modules

enrichment

Methods for the calculation of gene set enrichment statistics. The module contains overenrichment analysis, gene set variation analysis, gene set enrichment analysis (fgsea and blitzGSEA), mitch multi-dimensional enrichment and decoupler-style linear model activity scores (ULM, MLM).

errors

Errors raised by bixverse-methods.

graph

Module contains all of the graph-based algorithms within bixverse-rs.

methods

This module contains Rust-based methods of various common bioinformatics methods, accelerated and optimised were possible via multi-threading and data structures with good cache locality

ontology

Methods that work on ontologies, think Gene Ontology or Disease/Phenotype ontologies with relationships like ancestry, part of, etc.

prelude

Re-exports for use crate::prelude::*: the core prelude plus the methods-level types.