All 305,250 crates, alphabetically

rsomics-fastq-trimFASTQ adapter / poly-G / poly-X / fixed-length trimming. Rust port of fastp's trim hot path with rayon-parallel SE + PE pipelines…201MIT OR Apache-2.0Command line utilitiesScience rsomics-fastq-umiFASTQ inline-UMI extract + stamp. Rust port of fastp's UMI processing — full --umi_loc set…56MIT OR Apache-2.0Command line utilitiesScience rsomics-fastq-utilsFASTQ utility toolkit — lightweight subcommands for counting, filtering, converting, and inspecting FASTQ files89MIT OR Apache-2.0 rsomics-fastq-validateValidate FASTQ format integrity (line counts, quality encoding)59MIT OR Apache-2.0 rsomics-fastqcPer-file FASTQ quality-control report (FastQC-equivalent: per-base quality, GC, N, length, duplication, overrepresented, adapter,…42MIT OR Apache-2.0Command line utilitiesScience rsomics-fastx-convertConvert between FASTA/FASTQ formats: fq2fa, fa2fq, fx2tab, tab2fx, Phred quality re-encoding35MIT OR Apache-2.0 rsomics-fastx-sortDeterministic FASTA sorting by abundance or length — port of vsearch --sortbysize / --sortbylength17MIT OR Apache-2.0 rsomics-fclusterForm flat clusters from a hierarchical linkage matrix — scipy.cluster.hierarchy.fcluster (distance / maxclust / inconsistent /…60MIT OR Apache-2.0 rsomics-featurecountsCount reads over genomic features (BAM + GFF) — Rust port of featureCounts (Subread)51MIT OR Apache-2.0 rsomics-filter-by-exprBoolean per-gene expression filter for a count matrix, edgeR filterByExpr-compatible49MIT OR Apache-2.0 rsomics-find-peaksPeak detection in 1-D signals — value-exact, faster port of scipy.signal.find_peaks20MIT OR Apache-2.0Command line utilitiesScience rsomics-flignerFligner-Killeen test for equal variances (rank-based, median/mean/trimmed centering) with the chi-squared p-value —…39MIT OR Apache-2.0Command line utilitiesScience rsomics-fm-indexFM-index over BWT + suffix array, with backward search / count / locate. Layer A primitive for the rsomics-* tool family.51MIT OR Apache-2.0Data structuresScience rsomics-fm-searchExact substring search in FASTA using FM-index — count or locate pattern occurrences33MIT OR Apache-2.0 rsomics-formatsMeta-crate re-exporting rsomics format-tool libraries by feature flag235MIT OR Apache-2.0 rsomics-fpkm-countCompute per-gene FPKM from a BAM + BED12 model — Rust port of RSeQC FPKM_count18MIT OR Apache-2.0 rsomics-fqgzChunked parallel-libdeflate gzip (or plain) FASTQ-record writer. Layer-A primitive shared by the rsomics-* fastq-* tools.239MIT OR Apache-2.0Science rsomics-fragment-sizePaired-end insert-size distribution from a BAM: histogram TSV + summary with ATAC nucleosome fractions38MIT OR Apache-2.0 rsomics-freesasaSolvent-accessible surface area from a PDB via the Lee-Richards algorithm, with absolute + relative SASA (--rsa) per residue —…53MIT OR Apache-2.0 rsomics-freq-histCumulative and relative frequency histograms — value-exact to scipy.stats.cumfreq/relfreq20MIT OR Apache-2.0Command line utilitiesScience rsomics-friedman-testFriedman chi-square test for repeated measures — scipy.stats.friedmanchisquare equivalent, value-exact36MIT OR Apache-2.0Command line utilitiesScience rsomics-gaussian-filterValue-exact Gaussian blur — port of skimage.filters.gaussian / scipy.ndimage.gaussian_filter38MIT OR Apache-2.0Command line utilitiesScience rsomics-gc-skewWindowed GC-skew (G-C)/(G+C) per non-overlapping window — port of Bio.SeqUtils.GC_skew20MIT OR Apache-2.0Command line utilitiesScience rsomics-gc-windowsCompute per-window GC content across a FASTA reference — BED output for CNV/WGS normalization36MIT OR Apache-2.0 rsomics-gc123G+C content by codon position (overall + positions 1/2/3) of nucleotide sequences — Bio.SeqUtils.GC123 equivalent17MIT OR Apache-2.0 rsomics-genebody-coverageGene-body coverage profile (5'→3') for RNA-seq bias QC — Rust port of RSeQC geneBody_coverage.py17MIT OR Apache-2.0 rsomics-generalized-degreeGeneralized degree for undirected graph nodes — value-exact port of networkx.generalized_degree58MIT OR Apache-2.0Command line utilitiesScience rsomics-gff-countCount features in GFF/GTF files16MIT OR Apache-2.0 rsomics-gff-filterFilter GFF/GTF annotations by feature type, source, or attribute regex16MIT OR Apache-2.0 rsomics-gff-grepFilter GFF/GTF features by attribute regex — extract genes by name14MIT OR Apache-2.0 rsomics-gff-headOutput the first N GFF/GTF features (preserving header)19MIT OR Apache-2.0 rsomics-gff-mergersomics-gff-merge — rsomics bioinformatics tool18MIT OR Apache-2.0 rsomics-gff-sortSort GFF/GTF by chromosome + position14MIT OR Apache-2.0 rsomics-gff-statsGFF/GTF feature statistics — count by type, source, chromosome17MIT OR Apache-2.0 rsomics-gff-to-bedConvert GFF/GTF features to BED intervals16MIT OR Apache-2.0 rsomics-gff-utilsGFF/GTF utility toolkit — count, filter, extract, sort, convert, and stats operations55MIT OR Apache-2.0 rsomics-glcm-textureGLCM texture analysis — scikit-image graycomatrix + graycoprops port: contrast, dissimilarity, homogeneity, energy, ASM,…20MIT OR Apache-2.0Command line utilitiesScience rsomics-global-efficiencyGlobal efficiency of an undirected graph — port of networkx.global_efficiency36MIT OR Apache-2.0Command line utilitiesScience rsomics-gmeanGeneralized means of a sample (geometric / harmonic / power) and geometric standard deviation — value-exact to…20MIT OR Apache-2.0Command line utilitiesScience rsomics-goldfeld-quandtGoldfeld-Quandt heteroscedasticity test — value-exact, faster port of statsmodels het_goldfeldquandt33MIT OR Apache-2.0Command line utilitiesScience rsomics-gradient-trajectoryGradient/trajectory ANOVA over ordination coordinates (QIIME-style microbiome trajectory analysis): per-group trajectory vectors…57MIT OR Apache-2.0Command line utilitiesScience rsomics-graph-assortativityDegree assortativity coefficient for undirected graphs — value-exact port of networkx.degree_assortativity_coefficient52MIT OR Apache-2.0Command line utilitiesScience rsomics-graph-centralityDegree, closeness, and harmonic centrality for undirected graphs — value-exact networkx equivalent61MIT OR Apache-2.0Command line utilitiesScience rsomics-graph-componentsConnected-components queries for undirected graphs — value-exact networkx equivalent (count, sizes, largest, is-connected,…56MIT OR Apache-2.0Command line utilitiesScience rsomics-graph-cutsGraph-partition quality metrics (cut size, conductance, expansions) — value-exact port of networkx.algorithms.cuts56MIT OR Apache-2.0Command line utilitiesScience rsomics-graph-propertiesUndirected graph-property predicates (bipartite / eulerian / tree / forest / regular) — value-exact port of networkx boolean…58MIT OR Apache-2.0Command line utilitiesScience rsomics-graph-shortest-pathsShortest-path metrics for undirected graphs — value-exact networkx equivalent (diameter, radius, average, eccentricity, center,…69MIT OR Apache-2.0Command line utilitiesScience rsomics-greedy-colorGreedy graph coloring: value-exact port of networkx.greedy_color55MIT OR Apache-2.0Command line utilitiesScience rsomics-grey-morphologyGrayscale morphological erosion/dilation/opening/closing with flat rectangular footprint — value-exact port of scikit-image gray…39MIT OR Apache-2.0Command line utilitiesScience rsomics-group-centralityGroup betweenness / closeness / degree centrality of a node set in an undirected graph — value-exact networkx equivalent…58MIT OR Apache-2.0Command line utilitiesScience rsomics-haplotype-diversityHaplotype diversity (Nei 1987) from a phased VCF, genome-wide and in moving SNP windows20MIT OR Apache-2.0 rsomics-hausdorffDirected and symmetric Hausdorff distance between point clouds36MIT OR Apache-2.0Command line utilitiesScience rsomics-helpFamily-wide `--help` renderer for rsomics-* CLIs: figlet banner with gradient, section helpers, plain / JSON modes for AI…5,142MIT OR Apache-2.0Command-line interface rsomics-het-testsBreusch-Pagan (Koenker) and White Lagrange-multiplier tests for heteroscedasticity on OLS residuals — value-exact statsmodels…36MIT OR Apache-2.0Command line utilitiesScience rsomics-hmmHidden Markov Model inference (Viterbi / forward / backward) for the rsomics-* tool family. Layer A primitive.51MIT OR Apache-2.0Science rsomics-hmm-decodeViterbi-decode observation sequences with a discrete HMM — chromatin state, gene finding, CpG islands33MIT OR Apache-2.0 rsomics-hommolaHommola et al. (2009) host-parasite cospeciation permutation test, scikit-bio compatible37MIT OR Apache-2.0 rsomics-iccIntraclass correlation (ICC) — value-exact port of pingouin/psych ICC(1,1)/ICC(A,1)/ICC(C,1)/ICC(1,k)/ICC(A,k)/ICC(C,k), faster…20MIT OR Apache-2.0Command line utilitiesScience rsomics-igzipMinimal Quadrant-② FFI wrapper over Intel ISA-L igzip for fast gzip decompression. Isolated unsafe surface; all consumers stay…389MIT OR Apache-2.0Science rsomics-ilrIsometric log-ratio (ILR) transform of a composition table and its inverse (--inverse) — scikit-bio skbio.stats.composition.ilr /…56MIT OR Apache-2.0 rsomics-ilr-basisCustom-basis isometric log-ratio (ILR) transform: build an orthonormal balance basis from a sequential binary partition (SBP) or…37MIT OR Apache-2.0Command line utilitiesScience rsomics-image-entropyShannon entropy of a grayscale image — value-exact port of skimage.measure.shannon_entropy20MIT OR Apache-2.0Command line utilitiesScience rsomics-image-thresholdsAutomatic image thresholding (otsu, yen, triangle, multiotsu, mean) — value-exact port of scikit-image57MIT OR Apache-2.0Command line utilitiesScience rsomics-infercnvInfer copy-number variations from single-cell RNA-seq expression — Rust port of inferCNV18MIT OR Apache-2.0 rsomics-inner-distancemRNA-aware inner-distance distribution for paired-end RNA-seq — Rust port of RSeQC inner_distance.py39MIT OR Apache-2.0 rsomics-insertion-profilePer-position CIGAR-insertion rate along the read — Rust port of RSeQC insertion_profile.py18MIT OR Apache-2.0 rsomics-intervalsBED algebra + interval index + GFF/GTF interval extraction for the rsomics-* tool family. Layer A primitive.555MIT OR Apache-2.0Science rsomics-jarque-beraJarque-Bera normality test — scipy.stats.jarque_bera equivalent, value-exact37MIT OR Apache-2.0Command line utilitiesScience rsomics-junction-saturationSubsample-based splice-junction saturation analysis — Rust reimplementation of RSeQC junction_saturation.py18MIT OR Apache-2.0Science rsomics-k-clique-communitiesk-clique communities (clique percolation) of an undirected graph — networkx k_clique_communities equivalent17MIT OR Apache-2.0 rsomics-k-trussk-truss decomposition of undirected graphs (port of networkx.k_truss)36MIT OR Apache-2.0Command line utilitiesScience rsomics-kappaCohen's and Fleiss' kappa inter-rater agreement with variance, z-test and confidence interval — value-exact statsmodels…21MIT OR Apache-2.0Command line utilitiesScience rsomics-katz-centralityKatz centrality for biological networks — power-iteration port of networkx.katz_centrality56MIT OR Apache-2.0Command line utilitiesScience rsomics-kbinsPer-column binning (KBinsDiscretizer uniform + quantile) — value-exact scikit-learn equivalent36MIT OR Apache-2.0Command line utilitiesScience rsomics-kendall-tauKendall's tau rank correlation (tau-b/tau-c) with exact + asymptotic p-values — scipy.stats.kendalltau equivalent, value-exact20MIT OR Apache-2.0Command line utilitiesScience rsomics-kinshipKING-robust kinship coefficients between sample pairs from a PLINK1 fileset (plink2 --make-king-table)38MIT OR Apache-2.0Science rsomics-kmerK-mer encoding, canonicalisation, ntHash rolling hash, MurmurHash3, k-mer counting for the rsomics-* tool family. Layer A…246MIT OR Apache-2.0Science rsomics-kmer-distPairwise k-mer frequency distance between FASTA/FASTQ samples — Jaccard/Bray-Curtis/cosine36MIT OR Apache-2.0 rsomics-kpss-testKwiatkowski-Phillips-Schmidt-Shin (KPSS) stationarity test (statsmodels kpss equivalent)56MIT OR Apache-2.0 rsomics-kraken-reportParse and summarize Kraken2 report files — top taxa, diversity stats58MIT OR Apache-2.0 rsomics-kruskal-wallisKruskal-Wallis H-test for independent samples — scipy.stats.kruskal equivalent, value-exact35MIT OR Apache-2.0Command line utilitiesScience rsomics-ks-testTwo-sample Kolmogorov-Smirnov test (D, asymptotic + exact p) — scipy.stats.ks_2samp equivalent, value-exact152MIT OR Apache-2.0Command line utilitiesScience rsomics-label-statsPer-label reductions (sum/mean/variance/std/max/min/center-of-mass) — scipy.ndimage value-exact port35MIT OR Apache-2.0Command line utilitiesScience rsomics-ld-matrixCompute pairwise linkage disequilibrium (r²) from a genotype matrix75MIT OR Apache-2.0 rsomics-levene-testLevene's test for equal variances (Brown-Forsythe median/mean/trimmed) with the F-distribution p-value — scipy.stats.levene…29MIT OR Apache-2.0Command line utilitiesScience rsomics-limma-array-weightsEstimate per-sample (array) quality weights by REML for a log-expression matrix + design — a clean-room Rust reimplementation of…54MIT OR Apache-2.0 rsomics-limma-decide-testsClassify each gene × contrast as up/down/notsig from an eBayes-style results table — a clean-room Rust reimplementation of…58MIT OR Apache-2.0 rsomics-limma-diff-spliceDifferential exon usage / alternative splicing from a fitted linear model — a clean-room Rust reimplementation of limma's…53MIT OR Apache-2.0 rsomics-limma-duplicate-correlationREML consensus intra-block (duplicate-spot / technical-replicate) correlation for a log-expression matrix + design + block factor…57MIT OR Apache-2.0 rsomics-limma-ebayesPer-gene linear model fit (lmFit) plus empirical-Bayes moderated t-statistics (eBayes) for a log-expression matrix — a clean-room…96MIT OR Apache-2.0 rsomics-limma-proptruenullEstimate the proportion of true null hypotheses (pi0) from a vector of p-values — clean-room Rust reimplementation of limma's…54MIT OR Apache-2.0 rsomics-limma-squeeze-varEmpirical-Bayes shrinkage of a vector of gene variances toward a fitted scaled-F prior (limma squeezeVar / fitFDist) — a…54MIT OR Apache-2.0 rsomics-limma-treatModerated t-test against a log-fold-change threshold (limma treat + topTreat) for a log-expression matrix — a clean-room Rust…77MIT OR Apache-2.0 rsomics-limma-voomavooma mean-variance modelling: precision weights for a log-expression matrix + design — a clean-room Rust reimplementation of…49MIT OR Apache-2.0 rsomics-link-predictionNeighborhood-overlap link-prediction scores (Jaccard, Adamic-Adar, resource allocation, preferential attachment,…74MIT OR Apache-2.0 rsomics-linkageAgglomerative hierarchical clustering linkage matrix — value-exact scipy.cluster.hierarchy.linkage (all 7 methods)20MIT OR Apache-2.0Command line utilitiesScience rsomics-linkage-statsLinkage matrix inspection: maxdists, maxinconsts, is-monotonic, leaders, is-valid-linkage37MIT OR Apache-2.0Command line utilitiesScience rsomics-linregressSimple ordinary-least-squares linear regression with the Student-t p-value and standard errors — value-exact…40MIT OR Apache-2.0Command line utilitiesScience rsomics-load-centralityLoad centrality (Newman betweenness) for undirected graphs — port of networkx.load_centrality38MIT OR Apache-2.0Command line utilitiesScience rsomics-local-efficiencyLocal efficiency of an undirected graph (port of networkx.local_efficiency)79MIT OR Apache-2.0Command line utilitiesScience rsomics-log-lossProbabilistic-classification metrics — log loss (cross-entropy) and Brier score — value-exact scikit-learn equivalent33MIT OR Apache-2.0Command line utilitiesScience rsomics-macsModel-based ChIP-seq peak caller — single-end no-control Rust port of MACS3 callpeak20MIT OR Apache-2.0Command line utilitiesScience rsomics-mann-whitneyMann-Whitney U rank test (asymptotic + exact) — scipy.stats.mannwhitneyu equivalent, value-exact35MIT OR Apache-2.0Command line utilitiesScience rsomics-mantelMantel test — permutation correlation between two distance matrices (Pearson/Spearman), scikit-bio compatible81MIT OR Apache-2.0 rsomics-matrix-statsRow/column summary statistics over a numeric matrix — value-exact Rust port of R matrixStats (median, var, sd, mean, min, max,…61MIT OR Apache-2.0 rsomics-max-flowMaximum-flow value of a capacitated directed graph via Dinic's algorithm — networkx maximum_flow_value equivalent17MIT OR Apache-2.0 rsomics-maximal-matchingMaximal matching on undirected graphs — value-exact port of networkx.maximal_matching56MIT OR Apache-2.0Command line utilitiesScience rsomics-mcnemarMcNemar's test (2×2 paired) and Cochran's Q (k-sample paired binary) — value-exact statsmodels equivalent37MIT OR Apache-2.0Command line utilitiesScience rsomics-medcoupleMedcouple robust skewness statistic (Brys-Hubert-Struyf)40MIT OR Apache-2.0Command line utilitiesScience rsomics-median-testMood's median test for two or more samples — scipy.stats.median_test equivalent, value-exact18MIT OR Apache-2.0Command line utilitiesScience rsomics-methyldackelPer-CpG methylation extraction from bisulfite-aligned BAM — Rust port of MethylDackel extract40MIT OR Apache-2.0Science rsomics-minimap2Long/short-read aligner — CLI wrapper of minimap2 FFI bindings (Quadrant ②)19MIT OR Apache-2.0 rsomics-mismatch-profilePer-base mismatch-rate profile from BAM MD tags — Rust port of RSeQC mismatch_profile.py19MIT OR Apache-2.0 rsomics-modelsPinned DL-model registry + per-OS cache + sha256-verify for the rsomics-* tool family. Layer A primitive.19MIT OR Apache-2.0Science rsomics-modularityNewman-Girvan modularity Q of a graph partition — value-exact port of networkx.community.modularity58MIT OR Apache-2.0Command line utilitiesScience rsomics-molecular-weightMolecular mass of DNA / RNA / protein sequences (circular, double-stranded, monoisotopic) — Bio.SeqUtils.molecular_weight…16MIT OR Apache-2.0 rsomics-momentsCentral moments of a sample (skew, kurtosis, k-th moment) — value-exact to scipy.stats.skew/kurtosis/moment20MIT OR Apache-2.0Command line utilitiesScience rsomics-mood-testMood's two-sample test for equal scale parameters — scipy.stats.mood equivalent, value-exact20MIT OR Apache-2.0Command line utilitiesScience rsomics-moral-graphMoral graph of a directed graph — value-exact networkx 3.6.1 equivalent (Buntine 1995)58MIT OR Apache-2.0Command line utilitiesScience rsomics-motif-scanScan FASTA sequences for IUPAC DNA motif occurrences — BED output of match positions34MIT OR Apache-2.0 rsomics-msa-trimTrim MSA columns by gap fraction — Rust replacement for trimAl -gt35MIT OR Apache-2.0 rsomics-multi-replaceMultiplicative zero-replacement of a compositional matrix (closure + zero→delta substitution, rows re-sum to 1) — scikit-bio…35MIT OR Apache-2.0 rsomics-multibam-summaryMulti-BAM per-bin / per-region read-count matrix — Rust port of deeptools multiBamSummary76MIT OR Apache-2.0 rsomics-multibigwig-summaryMulti-bigWig per-bin / per-region mean-signal matrix — Rust port of deeptools multiBigwigSummary61MIT OR Apache-2.0Command line utilitiesScience rsomics-nj-treeNeighbor-joining tree construction from a distance matrix — outputs Newick55MIT OR Apache-2.0 rsomics-node-agesPhylogenetic node-timing / lineage-through-time ages (node ages, coalescence ages) — value-exact DendroPy…21MIT OR Apache-2.0Command line utilitiesScience rsomics-node-redundancyBipartite node redundancy coefficient (Latapy-Magnien-Del Vecchio), a value-exact Rust port of networkx.bipartite.node_redundancy37MIT OR Apache-2.0Command line utilitiesScience rsomics-normalizerPer-sample (per-row) L1/L2/max normalization — value-exact scikit-learn Normalizer port20MIT OR Apache-2.0Command line utilitiesScience rsomics-normaltestD'Agostino-Pearson normality battery (normaltest / skewtest / kurtosistest) — value-exact scipy.stats port40MIT OR Apache-2.0Command line utilitiesScience rsomics-obrien-transformO'Brien variance-homogeneity transform — value-exact scipy.stats.obrientransform, for feeding into a one-way ANOVA on spread20MIT OR Apache-2.0Command line utilitiesScience rsomics-odds-ratioOdds ratio for a 2x2 table — conditional MLE / sample estimate with exact CI, value-exact scipy.stats.contingency.odds_ratio42MIT OR Apache-2.0Command line utilitiesScience rsomics-onion-layersOnion decomposition of undirected graphs — integer layer per node (port of networkx.onion_layers)35MIT OR Apache-2.0Command line utilitiesScience rsomics-order-filter1-D order-statistic / median filter over a boxcar window (scipy.signal.order_filter / medfilt equivalent)19MIT OR Apache-2.0 rsomics-page-trendPage's trend test (Page's L) for ordered alternatives — scipy.stats.page_trend_test equivalent, value-exact19MIT OR Apache-2.0Command line utilitiesScience rsomics-pagerankPageRank for undirected graphs — value-exact port of networkx.pagerank52MIT OR Apache-2.0Command line utilitiesScience rsomics-pairwise-distancePairwise distance matrices (pdist + cdist + squareform) — value-exact scipy.spatial.distance equivalent21MIT OR Apache-2.0Command line utilitiesScience rsomics-partition-qualityCoverage and performance of a graph partition — value-exact port of networkx.community.partition_quality54MIT OR Apache-2.0Command line utilitiesScience rsomics-pbsPopulation Branch Statistic (PBS / PBSn1) sweep scan over a 3-population VCF — scikit-allel allel.pbs compatible, value-exact36MIT OR Apache-2.0 rsomics-pcaPrincipal Component Analysis (PCA) of a feature/sample table — scikit-bio skbio.stats.ordination.pca equivalent (column centering…65MIT OR Apache-2.0 rsomics-pcoaPrincipal Coordinates Analysis (PCoA) of a symmetric distance matrix — scikit-bio skbio.stats.ordination.pcoa equivalent (Gower…54MIT OR Apache-2.0 rsomics-pcoa-biplotProject descriptor/feature vectors onto a PCoA ordination — scikit-bio skbio.stats.ordination.pcoa_biplot equivalent (Legendre &…37MIT OR Apache-2.0Command line utilitiesScience rsomics-pdb-chainExtract or split PDB chains — list, extract single chain, or split all into separate files38MIT OR Apache-2.0 rsomics-pdb-contactsResidue/atom contact pairs within a distance cutoff from a PDB, value-exact to Bio.PDB.NeighborSearch.search_all55MIT OR Apache-2.0Command line utilitiesScience rsomics-pdb-coreBiopython-faithful fixed-column PDB ATOM/HETATM parser with configurable altloc selection, shared by the rsomics structure tools91MIT OR Apache-2.0Parser implementationsScience rsomics-pdb-dihedralsPer-residue protein backbone (phi/psi/omega) and side-chain (chi1-chi5) torsion angles from a PDB53MIT OR Apache-2.0Command line utilitiesScience rsomics-pdb-geometryGlobal geometric descriptors of a protein structure (center of mass, radius of gyration, bounding box, mass) from a PDB38MIT OR Apache-2.0Command line utilitiesScience rsomics-pdb-hsexposureHalf-sphere exposure (HSE-alpha, HSE-beta) and Ca contact number per residue from a PDB55MIT OR Apache-2.0Command line utilitiesScience rsomics-pdb-superposeKabsch least-squares superposition of two index-paired atom sets from PDB — rotation, translation, RMSD, à la Bio.PDB.Superimposer36MIT OR Apache-2.0Command line utilitiesScience rsomics-peak-annotateAnnotate ChIP/ATAC peaks with nearest gene, TSS distance, and genomic-feature category — Rust port of Bioconductor ChIPseeker…37MIT OR Apache-2.0Command line utilitiesScience rsomics-peak-countCount BAM reads per BED peak region — ChIP-seq/ATAC-seq QC and quantification48MIT OR Apache-2.0 rsomics-percentileInverse percentile operations (percentileofscore, scoreatpercentile) — value-exact to scipy.stats33MIT OR Apache-2.0Command line utilitiesScience rsomics-permanovaPERMANOVA (Anderson 2001) — pseudo-F test for group differences from a distance matrix, with a permutation p-value; scikit-bio…73MIT OR Apache-2.0 rsomics-permdispPERMDISP (Anderson 2006) — test of homogeneity of multivariate group dispersions from a distance matrix (the betadisper analog),…75MIT OR Apache-2.0 rsomics-pgenPLINK1 .bed / .bim / .fam genotype-matrix reader + writer for the rsomics-* tool family. Layer A primitive.535MIT OR Apache-2.0Science rsomics-phydivGeneralized phylogenetic alpha-diversity (rooted/unrooted, abundance-weighted PD) from a feature count table + a Newick tree —…48MIT OR Apache-2.0 rsomics-phylo-treePhylogenetic tree type + Newick parser/emitter for the rsomics-* tool family. Layer A primitive.226MIT OR Apache-2.0Science rsomics-pileupCoordinate-sorted BAM pileup engine (htslib bam_plp port): per-position read columns with CIGAR-resolved qpos/indel/head/tail and…98MIT OR Apache-2.0Science rsomics-plink-assocPLINK1 case/control association test (chi-squared + trend + linear regression)40MIT OR Apache-2.0 rsomics-plink-check-sexPLINK1 X-chromosome sex check: per-sample inbreeding F and male/female imputation (plink --check-sex)41MIT OR Apache-2.0 rsomics-plink-clusterIBS-based complete-linkage clustering of samples (plink --cluster)17MIT OR Apache-2.0 rsomics-plink-epistasisPLINK1 pairwise SNP×SNP logistic-regression interaction scan (plink --epistasis)17MIT OR Apache-2.0 rsomics-plink-flip-scanPLINK1 --flip-scan: LD-sign strand-inconsistency QC scan (per-SNP positive/negative correlation matches between cases and…16MIT OR Apache-2.0 rsomics-plink-freqPLINK1 per-variant allele frequency report (plink --freq)18MIT OR Apache-2.0 rsomics-plink-freqxPLINK1 per-variant genotype-class counts (plink --freqx)37MIT OR Apache-2.0 rsomics-plink-grmGCTA-style genetic relationship matrix from a PLINK1 fileset (plink2 --make-rel / --make-grm)19MIT OR Apache-2.0Science rsomics-plink-hetPLINK1 method-of-moments inbreeding coefficient F per sample (plink --het)57MIT OR Apache-2.0 rsomics-plink-homozygPLINK1 runs of homozygosity via the scanning-window algorithm (plink --homozyg)19MIT OR Apache-2.0 rsomics-plink-ibcPLINK1 method-of-moments inbreeding coefficients Fhat1/Fhat2/Fhat3 per sample (plink --ibc)41MIT OR Apache-2.0 rsomics-plink-ioPLINK1 binary .bed/.bim/.fam reader: allele-freq, missingness, HWE, VCF/012 export20MIT OR Apache-2.0 rsomics-plink-ldPairwise LD (r²) computation and LD matrix export from PLINK1 binary filesets19MIT OR Apache-2.0 rsomics-plink-linearQuantitative-trait GWAS by per-variant additive OLS (plink --linear)39MIT OR Apache-2.0 rsomics-plink-logisticBinary case/control GWAS by per-variant logistic regression (plink --logistic)42MIT OR Apache-2.0 rsomics-plink-mendelPLINK1 Mendel error detection in trios and parent-offspring duos (plink --mendel)17MIT OR Apache-2.0 rsomics-plink-missingPer-sample and per-variant genotype missingness from a PLINK1 binary fileset (plink --missing)41MIT OR Apache-2.0 rsomics-plink-modelPLINK1 full case/control genotypic association (--model): GENO, TREND, ALLELIC, DOM, REC33MIT OR Apache-2.0 rsomics-plink-pcaPCA and GRM computation from PLINK1 binary filesets using faer EVD38MIT OR Apache-2.0 rsomics-plink-pruneLD pruning from PLINK1 binary filesets (--indep-pairwise)20MIT OR Apache-2.0 rsomics-plink-recodeAdditive (0/1/2) genotype dosage matrix export from PLINK1 binary filesets (plink --recode A)20MIT OR Apache-2.0 rsomics-plink-scorePLINK1 polygenic allele-dosage scoring per sample (plink --score)40MIT OR Apache-2.0 rsomics-plink-tdtPLINK1 transmission disequilibrium test for trios (plink --tdt)39MIT OR Apache-2.0 rsomics-plink-test-missingDifferential genotype-missingness test between cases and controls (plink --test-missing)40MIT OR Apache-2.0 rsomics-plot-coverageGenome-wide coverage distribution of one or more BAMs: per-bin sampled read counts (--out-raw-counts) plus per-sample summary…52MIT OR Apache-2.0Command line utilitiesScience rsomics-point-biserialPoint-biserial correlation between a binary and a continuous variable with the Pearson two-sided p-value —…19MIT OR Apache-2.0Command line utilitiesScience rsomics-polynomial-featuresPolynomial / interaction feature expansion of a dense matrix (sklearn PolynomialFeatures equivalent)16MIT OR Apache-2.0 rsomics-popgen-corePopulation-genetics primitives: π, Watterson's θ, Tajima's D, Hardy-Weinberg exact, LD r². Layer A primitive.49MIT OR Apache-2.0Science rsomics-popgen-fstatsPatterson's admixture f-statistics from VCF: D (ABBA-BABA), f2, f3, f4 with block-jackknife SE/Z (scikit-allel value-exact)20MIT OR Apache-2.0 rsomics-popgen-garudhGarud H1/H12/H123/H2H1 haplotype-homozygosity soft-sweep statistics from a phased VCF, genome-wide and in moving SNP windows20MIT OR Apache-2.0 rsomics-popgen-ihsEHH-based single-population selection scans — nSL and iHS (integrated haplotype score) — from a phased VCF, value-exact to…20MIT OR Apache-2.0 rsomics-popgen-windowedWindowed genome-scan diversity statistics from a VCF: nucleotide diversity pi, Dxy divergence, Watterson's theta, Tajima's D,…37MIT OR Apache-2.0 rsomics-popgen-xpehhCross-population EHH selection scans — XP-EHH and XP-nSL — from two phased VCF populations, value-exact to scikit-allel19MIT OR Apache-2.0 rsomics-power-divergenceCressie-Read power divergence goodness-of-fit test — scipy.stats.power_divergence/chisquare equivalent, value-exact33MIT OR Apache-2.0Command line utilitiesScience rsomics-proportion-effectsizeCohen's h effect size for two proportions (arcsine transform) — value-exact statsmodels.stats.proportion.proportion_effectsize,…20MIT OR Apache-2.0Command line utilitiesScience rsomics-proportions-ztestProportion z-test (one- and two-sample) with normal p-value — value-exact statsmodels.stats.proportion.proportions_ztest…33MIT OR Apache-2.0Command line utilitiesScience rsomics-prot-paramProtein physicochemical properties — instability index, GRAVY, aromaticity, amino-acid composition and molecular weight —…81MIT OR Apache-2.0 rsomics-pvalue-adjustMultiple-testing correction for a column of p-values — the full R p.adjust method set…59MIT OR Apache-2.0Command line utilitiesScience rsomics-pwmantelPairwise Mantel test across N distance matrices (Pearson/Spearman + permutation p), scikit-bio pwmantel compatible53MIT OR Apache-2.0 rsomics-quantile-normQuantile normalization of a gene x sample count matrix (limma normalizeQuantiles)49MIT OR Apache-2.0 rsomics-quantile-transformQuantile transformer — value-exact scikit-learn QuantileTransformer port mapping features to uniform or normal distributions37MIT OR Apache-2.0Command line utilitiesScience rsomics-rankdataAssign ranks to data with tie handling (average/min/max/dense/ordinal) — value-exact to scipy.stats.rankdata20MIT OR Apache-2.0Command line utilitiesScience rsomics-ranksumsWilcoxon rank-sum test (normal approximation) — scipy.stats.ranksums equivalent, value-exact21MIT OR Apache-2.0Command line utilitiesScience