cyanea-omics

Data structures for genomics, transcriptomics, variant analysis, single-cell biology, and spatial transcriptomics.

434 unit tests + 2 doc tests.

What's Inside

• Genomic coordinates -- GenomicPosition, GenomicInterval, Strand (0-based half-open)
• Interval operations -- IntervalSet with overlap queries, merging, coverage computation
• Interval tree -- augmented BST with O(log n + k) overlap, nearest/preceding/following queries
• Coverage vectors -- RLE-encoded genome-wide depth from intervals
• Expression matrices -- dense features x samples matrix with named rows/columns
• Sparse matrices -- COO-format with CSR conversion for high-dimensional data
• Variant types -- VCF-style Variant with VariantType, Zygosity, filters
• Variant annotation -- coding consequence prediction (missense/nonsense/frameshift/splice), HGVS notation, SIFT-style scoring
• Gene annotations -- Gene / Transcript / Exon hierarchy with biotypes
• AnnData container -- single-cell data with obs/var metadata, obsm/varm embeddings, layers, obsp, uns
• HDF5 I/O -- read/write .h5ad files (dense and CSR sparse, metadata, embeddings)
• Zarr I/O -- read/write Zarr v3 directories (pure Rust, same feature set as h5ad)
• OTU/ASV tables -- abundance tables with rarefaction, filtering, taxonomic collapse
• Network biology -- weighted graphs, degree/betweenness/closeness centrality, Louvain communities
• Haplotype analysis -- EM phasing, haplotype block detection, diversity statistics
• Genome arithmetic -- intersect, union, subtract, complement, closest, window, Jaccard
• Liftover -- UCSC chain file parsing, coordinate remapping between assemblies
• CNV analysis -- CBS segmentation, B-allele frequency, SV breakpoint detection, segment merging
• Methylation -- bisulfite conversion, CpG site calling, DMRs, CpG island detection
• Spatial transcriptomics -- Delaunay/kNN spatial graphs, Moran's I, Geary's C, co-occurrence, ligand-receptor
• Single-cell pipeline -- normalize, HVG, kNN graph, Leiden/Louvain, diffusion map, DPT, PAGA, RNA velocity, markers, Harmony/ComBat/MNN integration

Quick Start

[dependencies]
cyanea-omics = { version = "0.1", features = ["zarr"] }

use cyanea_omics::{GenomicInterval, IntervalSet, Strand};

let intervals = vec![
    GenomicInterval::new("chr1", 100, 200, Strand::Plus),
    GenomicInterval::new("chr1", 150, 300, Strand::Plus),
];
let set = IntervalSet::from(intervals);
let merged = set.merge();

Feature Flags

Modules

See Also

• API Reference
• Usage Guide
• Architecture