cyanea-omics 0.1.0

Omics data structures for the Cyanea bioinformatics ecosystem
Documentation

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

Flag Default Description
std Yes Standard library support
wasm No WASM target marker
serde No Serialize/Deserialize derives
h5ad No HDF5 .h5ad I/O (requires system HDF5 1.10.x)
zarr No Zarr v3 directory I/O (pure Rust)
single-cell No Single-cell analysis pipeline (HVG, clustering, trajectory, markers, integration)

Modules

Module Description
genomic GenomicPosition, GenomicInterval, Strand
interval IntervalSet with overlap, merge, coverage
interval_tree Augmented BST with O(log n + k) overlap queries
coverage RLE coverage vectors
expr Dense expression matrix
sparse COO sparse matrix with CSR conversion
variant Variant, VariantType, Zygosity
variant_annotation Consequence prediction, HGVS notation, splice scoring
annotation Gene, Transcript, Exon hierarchy
single_cell AnnData container with typed metadata
h5ad HDF5 .h5ad reader/writer (feature-gated)
zarr Zarr v3 reader/writer (feature-gated)
otu OTU/ASV abundance tables
network Weighted graphs, centrality, Louvain
haplotype EM phasing, haplotype blocks
genome_arithmetic Intersect, union, subtract, complement, closest, window, Jaccard
liftover UCSC chain file parsing, coordinate liftover
cnv CBS segmentation, BAF, SV breakpoints
methylation CpG sites, DMRs, CpG islands, bisulfite conversion
spatial Spatial neighbor graphs, Moran's I, Geary's C, co-occurrence, ligand-receptor
sc_preprocess HVG, normalize, regress, doublet detection, gene scoring (feature-gated)
sc_cluster kNN graph, Leiden, Louvain, NMI, ARI (feature-gated)
sc_trajectory Diffusion map, DPT, PAGA, RNA velocity (feature-gated)
sc_markers Marker gene detection: t-test, Wilcoxon, logistic regression (feature-gated)
sc_integrate Harmony, ComBat, MNN, kBET/LISI metrics (feature-gated)

See Also