Crate cyanea_omics 

Omics data structures for the Cyanea bioinformatics ecosystem.

This crate provides core types for working with omics data:

• Genomic coordinates — Strand, GenomicPosition, GenomicInterval
• Interval collections — IntervalSet with overlap queries
• Expression matrices — Dense ExpressionMatrix (features × samples)
• Sparse matrices — SparseMatrix in COO format
• Variants — VCF-style Variant representation
• Gene annotations — Gene, Transcript, Exon hierarchy

Quick start

use cyanea_omics::ExpressionMatrix;
use cyanea_core::Summarizable;

let matrix = ExpressionMatrix::new(
    vec![vec![1.0, 2.0], vec![3.0, 4.0]],
    vec!["gene1".into(), "gene2".into()],
    vec!["sample_a".into(), "sample_b".into()],
).unwrap();

assert_eq!(matrix.shape(), (2, 2));
assert_eq!(matrix.get(0, 1), Some(2.0));
assert_eq!(matrix.summary(), "ExpressionMatrix: 2 features \u{00d7} 2 samples");

Re-exports

pub use cnv::BafSegment;

pub use cnv::CbsConfig;

pub use cnv::CnvSegment;

pub use cnv::SvBreakpoint;

pub use cnv::SvType;

pub use cnv::baf_segmentation;

pub use cnv::circular_binary_segmentation;

pub use cnv::detect_sv_breakpoints;

pub use cnv::merge_cnv_segments;

pub use genomic::GenomicInterval;

pub use genomic::GenomicPosition;

pub use genomic::Strand;

pub use interval::IntervalSet;

pub use interval_tree::Interval;

pub use interval_tree::IntervalTree;

pub use coverage::RleCoverage;

pub use expr::ExpressionMatrix;

pub use sparse::SparseMatrix;

pub use variant::Variant;

pub use variant::VariantFilter;

pub use variant::VariantType;

pub use variant::Zygosity;

pub use annotation::Exon;

pub use annotation::Gene;

pub use annotation::GeneType;

pub use annotation::Transcript;

pub use variant_annotation::AnnotationConfig;

pub use variant_annotation::Consequence;

pub use variant_annotation::SpliceScore;

pub use variant_annotation::VariantEffect;

pub use variant_annotation::annotate_variant;

pub use variant_annotation::annotate_variants;

pub use variant_annotation::score_splice_disruption;

pub use single_cell::ColumnData;

pub use genome_arithmetic::ClosestResult;

pub use genome_arithmetic::GenomeInfo;

pub use genome_arithmetic::JaccardStats;

pub use genome_arithmetic::StrandMode;

pub use genome_arithmetic::closest;

pub use genome_arithmetic::complement;

pub use genome_arithmetic::genome_info;

pub use genome_arithmetic::intersect;

pub use genome_arithmetic::intersect_report_a;

pub use genome_arithmetic::jaccard;

pub use genome_arithmetic::jaccard_stats;

pub use genome_arithmetic::make_sliding_windows;

pub use genome_arithmetic::make_windows;

pub use genome_arithmetic::merge;

pub use genome_arithmetic::subtract;

pub use genome_arithmetic::union;

pub use genome_arithmetic::windows_around;

pub use liftover::ChainFile;

pub use liftover::LiftoverResult;

pub use liftover::liftover;

pub use liftover::liftover_batch;

pub use liftover::parse_chain;

pub use methylation::CpgIsland;

pub use methylation::CpgSite;

pub use methylation::DmRegion;

pub use methylation::DmrConfig;

pub use methylation::bisulfite_convert;

pub use methylation::call_methylation;

pub use methylation::find_cpg_islands;

pub use methylation::find_dmrs;

pub use spatial::CooccurrenceResult;

pub use spatial::GearysC;

pub use spatial::LrInteraction;

pub use spatial::SpatialAutocorrelation;

pub use spatial::SpatialGraph;

pub use spatial::SpatialPoint;

pub use spatial::cooccurrence;

pub use spatial::delaunay_neighbors;

pub use spatial::gearys_c;

pub use spatial::knn_spatial_neighbors;

pub use spatial::ligand_receptor_score;

pub use spatial::morans_i;

pub use otu::OtuTable;

pub use network::CentralityScores;

pub use network::Community;

pub use network::Graph;

pub use haplotype::haplotype_blocks;

pub use haplotype::haplotype_diversity;

pub use haplotype::phase_em;

pub use haplotype::Haplotype;

pub use haplotype::HaplotypeBlock;

pub use haplotype::PhasedGenotypes;

Modules

annotation

Gene, transcript, and exon annotation types.

cnv

Copy number and structural variant analysis.

coverage

Run-length encoded coverage vectors for memory-efficient genome-wide depth.

expr

Dense expression matrix for bulk omics data.

genome_arithmetic

BEDTools-style genome arithmetic on genomic intervals.

genomic

Genomic primitives — strand, position, and interval types.

haplotype

Haplotype analysis — EM phasing, haplotype blocks, and haplotype diversity.

interval

Sorted interval collection with overlap queries.

interval_tree

Static augmented interval tree for fast overlap queries.

liftover

UCSC chain file parsing and genomic coordinate liftover.

methylation

Methylation analysis — CpG sites, differentially methylated regions, and CpG islands.

network

Network biology — weighted graphs, centrality metrics, and community detection.

otu

OTU/ASV table operations for metagenomics.

single_cell

AnnData-like container for single-cell omics data.

sparse

Coordinate-format (COO) sparse matrix.

spatial

Spatial transcriptomics analysis — neighbor graphs, spatial autocorrelation, co-occurrence, and ligand-receptor interaction scoring.

variant

Genomic variant representation (VCF-style).

variant_annotation

Variant effect prediction and annotation.