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All 305,250 crates, alphabetically
Data as of 2026-07-25 (crates.io database dump, timestamp 2026-07-25T02:00:36Z). Source: crates.io · db-dump.tar.gz · methodology & corrections.
rsomics-bam-samplesList @RG sample names from one or more BAM headers — Rust port of samtools samples65MIT OR Apache-2.0
rsomics-bam-signalBinned BAM → bedGraph/bigWig signal track — Rust port of deeptools bamCoverage100MIT OR Apache-2.0
rsomics-bam-sortBAM sorting by coordinate or read name — Rust port of samtools sort40MIT OR Apache-2.0
rsomics-bam-splitSplit BAM by read group — Rust port of samtools split42MIT OR Apache-2.0
rsomics-bam-split-peSplit a paired-end BAM into read-1, read-2 and unmapped BAMs — Rust port of RSeQC split_paired_bam.py19MIT OR Apache-2.0
rsomics-bam-statsComprehensive alignment statistics from BAM — Rust port of samtools stats58MIT OR Apache-2.0
rsomics-bam-strandednessInfer RNA-seq library strand protocol from BAM + BED12 gene model — Rust port of RSeQC infer_experiment.py72MIT OR Apache-2.0
rsomics-bam-subsampleRandom downsampling of BAM/SAM records by fraction or target count52MIT OR Apache-2.0
rsomics-bam-targetcutIdentify target intervals from pileup depth — Rust port of samtools targetcut40MIT OR Apache-2.0
rsomics-bam-to-bedConvert BAM alignments to BED6 format — Rust port of bedtools bamtobed54MIT OR Apache-2.0
rsomics-bam-to-fastqExtract FASTQ reads from BAM — Rust port of samtools fastq63MIT OR Apache-2.0
rsomics-bam-viewView, filter, and convert SAM/BAM/CRAM alignments — Rust port of samtools view41MIT OR Apache-2.0
rsomics-bamioParallel-BGZF BAM reader/writer + raw-record edit shared by the rsomics-bam-* tool family. Layer A primitive.1,804MIT OR Apache-2.0
rsomics-barcode-rankBarcode rank statistics from a counts-per-barcode file — knee plot data for single-cell QC35MIT OR Apache-2.0
rsomics-barnard-exactBarnard's unconditional exact test for a 2x2 contingency table (pooled/unpooled Wald statistic, nuisance-parameter maximization)…18MIT OR Apache-2.0
rsomics-bartlett-testBartlett's test for equal variances — scipy.stats.bartlett equivalent, value-exact35MIT OR Apache-2.0
rsomics-bayes-mvsBayesian confidence intervals for the mean, variance, and std of a sample — value-exact to scipy.stats.bayes_mvs / mvsdist36MIT OR Apache-2.0
rsomics-bbdukK-mer-based contaminant removal + adapter/quality trimming for FASTQ — independent clean-room Rust reimplementation of BBDuk…36MIT OR Apache-2.0
rsomics-bbiPure-Rust bigWig/BBI reader and writer: header, chromosome B-tree, R-tree interval search, bedGraph/varStep/fixedStep section…340MIT OR Apache-2.0
rsomics-bed-annotateAnnotate BED intervals with per-file overlap fractions from N annotation files — Rust port of bedtools annotate69MIT OR Apache-2.0
rsomics-bed-closestFind the closest feature in B for each interval in A — bedtools closest equivalent86MIT OR Apache-2.0
rsomics-bed-clusterCluster overlapping BED intervals and append a cluster ID — bedtools cluster equivalent52MIT OR Apache-2.0
rsomics-bed-complementCompute the complement of a BED file — intervals not covered by any feature (bedtools complement equivalent)94MIT OR Apache-2.0
rsomics-bed-countCount intervals in BED files38MIT OR Apache-2.0
rsomics-bed-coveragePer-interval coverage depth/breadth of B features onto A — Rust port of bedtools coverage70MIT OR Apache-2.0
rsomics-bed-expandReplicate BED/TSV lines by expanding comma-separated column values — Rust port of bedtools expand70MIT OR Apache-2.0
rsomics-bed-fisherFisher's exact test for overlap significance between two BED interval sets — bedtools fisher equivalent38MIT OR Apache-2.0
rsomics-bed-flankCreate flanking BED intervals for each feature — bedtools flank equivalent90MIT OR Apache-2.0
rsomics-bed-genomecovGenome-wide coverage from BED intervals — bedgraph, per-base depth, and histogram modes87MIT OR Apache-2.0
rsomics-bed-getfastaExtract FASTA sequences for BED intervals — bedtools getfasta equivalent69MIT OR Apache-2.0
rsomics-bed-groupbyGroup tab-delimited rows by key columns and aggregate value columns — bedtools groupby equivalent73MIT OR Apache-2.0
rsomics-bed-intersectIntersect BED intervals — bedtools intersect equivalent89MIT OR Apache-2.0
rsomics-bed-jaccardCompute Jaccard similarity statistic between two BED files — bedtools jaccard equivalent108MIT OR Apache-2.0
rsomics-bed-lenBED interval lengths39MIT OR Apache-2.0
rsomics-bed-makewindowsTile a genome into fixed-size BED windows — bedtools makewindows equivalent54MIT OR Apache-2.0
rsomics-bed-mapAggregate column values from B intervals overlapping each A interval — bedtools map equivalent85MIT OR Apache-2.0
rsomics-bed-mergeMerge overlapping BED intervals — bedtools merge equivalent93MIT OR Apache-2.0
rsomics-bed-midpointCollapse BED intervals to their midpoints — outputs a 1-bp BED record at floor((start+end)/2)54MIT OR Apache-2.0
rsomics-bed-multicovCount reads from multiple BAM files overlapping BED intervals — bedtools multicov equivalent57MIT OR Apache-2.0
rsomics-bed-multiinterMulti-file interval intersection depth — bedtools multiinter equivalent52MIT OR Apache-2.0
rsomics-bed-nucPer-interval nucleotide composition from BED + FASTA — Rust port of bedtools nuc72MIT OR Apache-2.0
rsomics-bed-overlapCompute overlap or distance between two interval columns — bedtools overlap equivalent57MIT OR Apache-2.0
rsomics-bed-randomGenerate random BED intervals — bedtools random equivalent39MIT OR Apache-2.0
rsomics-bed-reldistCompute relative distances between two BED interval sets — bedtools reldist equivalent39MIT OR Apache-2.0
rsomics-bed-sampleSample random BED records using reservoir sampling — bedtools sample equivalent53MIT OR Apache-2.0
rsomics-bed-shiftShift BED coordinates by a fixed offset — bedtools shift equivalent71MIT OR Apache-2.0
rsomics-bed-shuffleRandomly relocate BED intervals within a genome — bedtools shuffle equivalent69MIT OR Apache-2.0
rsomics-bed-slopExtend BED intervals by N bp on each side, clamping to chromosome bounds — bedtools slop equivalent72MIT OR Apache-2.0
rsomics-bed-sortSort BED intervals by chromosome and start — bedtools sort equivalent59MIT OR Apache-2.0
rsomics-bed-spacingReport gap lengths between consecutive BED intervals — bedtools spacing equivalent59MIT OR Apache-2.0
rsomics-bed-splitSplit a BED file into N equal-base-pair or equal-record parts — Rust port of bedtools split51MIT OR Apache-2.0
rsomics-bed-statsBED interval statistics — total count, total bases, mean/median length37MIT OR Apache-2.0
rsomics-bed-subtractSubtract BED intervals — bedtools subtract equivalent72MIT OR Apache-2.0
rsomics-bed-summaryStatistical summary of BED intervals per chromosome — Rust port of bedtools summary72MIT OR Apache-2.0
rsomics-bed-to-gffConvert BED intervals to GFF3 format38MIT OR Apache-2.0
rsomics-bed-total-bpCount total base-pairs covered by BED intervals (sum of end - start)37MIT OR Apache-2.0
rsomics-bed-unionbedgCombine multiple sorted BedGraph files into one — bedtools unionbedg equivalent53MIT OR Apache-2.0
rsomics-bed-uniqueRemove duplicate BED intervals (same chrom, start, end)37MIT OR Apache-2.0
rsomics-bed-utilsBED utility toolkit — sort, merge, intersect, subtract, complement, stats, convert, and 40+ more operations88MIT OR Apache-2.0
rsomics-bed-validateValidate BED file format: check field counts, coordinate ordering, and integer parsing39MIT OR Apache-2.0
rsomics-bed-windowFind BED features within a window of A intervals — bedtools window equivalent66MIT OR Apache-2.0
rsomics-bed12-to-bed6Break BED12 block annotations into discrete BED6 intervals — Rust port of bedtools bed12tobed655MIT OR Apache-2.0
rsomics-bed12tobed6Split BED12 features into discrete BED6 intervals — bedtools bed12tobed6 equivalent36MIT OR Apache-2.0
rsomics-beta-diversityPairwise between-sample beta-diversity distance matrix (Bray-Curtis, Jaccard, Euclidean, Canberra, Manhattan) from a feature…61MIT OR Apache-2.0
rsomics-betweenness-centralityBetweenness centrality for undirected graphs — value-exact networkx equivalent (Brandes 2001)53MIT OR Apache-2.0
rsomics-bgzipBlock-compress or decompress a file in BGZF — Rust port of htslib bgzip19MIT OR Apache-2.0
rsomics-biconnectivityBiconnectivity family (bridges, articulation points, biconnected components) — value-exact port of…38MIT OR Apache-2.0
rsomics-bigwig-averagePer-bin average of N bigWig files as a bedGraph track — Rust port of deepTools bigwigAverage36MIT OR Apache-2.0
rsomics-bigwig-comparePer-bin comparison of two bigWig files as a bedGraph track — Rust port of deeptools bigwigCompare82MIT OR Apache-2.0
rsomics-binned-statisticPer-bin statistic of a second variable (mean/std/median/count/sum/min/max) — value-exact to scipy.stats.binned_statistic36MIT OR Apache-2.0
rsomics-binned-statistic-2d2D per-bin statistic (mean/std/median/count/sum/min/max) — value-exact to scipy.stats.binned_statistic_2d20MIT OR Apache-2.0
rsomics-binom-testExact binomial test (k successes in n trials vs hypothesized p) with Clopper-Pearson and Wilson confidence intervals —…19MIT OR Apache-2.0
rsomics-bioenvBIO-ENV / BEST — subset of environmental variables maximally rank-correlated with a community distance matrix (Clarke & Ainsworth…89MIT OR Apache-2.0
rsomics-bipartite-clusteringBipartite clustering coefficients: Latapy per-node (dot/min/max), average, and Robins-Alexander — value-exact networkx 3.6.1…54MIT OR Apache-2.0
rsomics-boschloo-exactBoschloo's 2x2 unconditional exact test (uniformly more powerful than Fisher's exact) — scipy.stats.boschloo_exact equivalent,…41MIT OR Apache-2.0
rsomics-boxcoxBox-Cox power transform, log-likelihood, and MLE/Pearson optimal lambda — value-exact to scipy.stats.boxcox22MIT OR Apache-2.0
rsomics-brunner-munzelBrunner-Munzel test (generalized Wilcoxon, unequal variances) — scipy.stats.brunnermunzel equivalent, value-exact18MIT OR Apache-2.0
rsomics-caiCodon Adaptation Index (Sharp & Li 1987) — value-exact port of biopython Bio.SeqUtils.CodonAdaptationIndex41MIT OR Apache-2.0
rsomics-ccaCanonical (constrained) Correspondence Analysis of a community count table on environmental constraints — scikit-bio…52MIT OR Apache-2.0
rsomics-cell-filterFilter cells by QC metrics — min genes, min UMIs, max mito fraction from a barcode stats TSV38MIT OR Apache-2.0
rsomics-chi-squareChi-square test of independence on a contingency table (with G-test and Fisher exact 2x2) — scipy.stats.chi2_contingency /…36MIT OR Apache-2.0
rsomics-chordalGraph chordality test and chordal maximal-clique enumeration via maximum cardinality search — value-exact port of…40MIT OR Apache-2.0
rsomics-circmeanCircular mean / variance / standard deviation of angle observations — scipy.stats.circmean/circvar/circstd equivalent, value-exact37MIT OR Apache-2.0
rsomics-classification-metricsLabel-based classification metrics — MCC, balanced accuracy, precision/recall/F1 (macro/micro/weighted), confusion matrix,…20MIT OR Apache-2.0
rsomics-clipping-profilePer-position soft-clipping profile from a BAM — Rust port of RSeQC clipping_profile.py18MIT OR Apache-2.0
rsomics-cliquesMaximal-clique family (find_cliques, node_clique_number, number_of_cliques, clique number) — value-exact port of…37MIT OR Apache-2.0
rsomics-closeness-vitalityCloseness vitality of nodes in an undirected, unweighted graph — value-exact networkx 3.6.1 equivalent37MIT OR Apache-2.0
rsomics-clrCentered log-ratio (CLR) transform of a composition table and its inverse (--inverse) — scikit-bio skbio.stats.composition.clr /…57MIT OR Apache-2.0
rsomics-clustering-coefficientTriangle-based clustering metrics for undirected graphs — value-exact networkx equivalent (triangles, local/average clustering,…53MIT OR Apache-2.0
rsomics-clustering-metricsExternal cluster-validation metrics — ARI, Rand, NMI, AMI, mutual info, homogeneity, completeness, V-measure, Fowlkes-Mallows —…20MIT OR Apache-2.0
rsomics-cmhStratified 2×2 analysis (statsmodels StratifiedTable): Cochran-Mantel-Haenszel test, Mantel-Haenszel pooled odds/risk ratio, and…33MIT OR Apache-2.0
rsomics-combine-pvaluesCombine independent p-values (meta-analysis) — value-exact to scipy.stats.combine_pvalues…48MIT OR Apache-2.0
rsomics-commonShared primitives for every rsomics-* crate (errors, CLI scaffold, runner, progress, exit codes).7,807MIT OR Apache-2.0
rsomics-compute-gc-biasEstimate the GC-content bias of a BAM by comparing observed vs expected read counts per GC bin over a 2bit genome — Rust port of…51MIT OR Apache-2.0
rsomics-compute-matrixbigWig signal → score matrix over BED regions — Rust port of deeptools computeMatrix84MIT OR Apache-2.0
rsomics-condensationCondensation of a directed graph (contract each SCC into one node → DAG) — value-exact port of networkx.condensation52MIT OR Apache-2.0
rsomics-connectivityExact node/edge connectivity of an undirected graph — value-exact port of networkx.node_connectivity and…35MIT OR Apache-2.0
rsomics-consensusCompute consensus sequence from a multiple sequence alignment — majority-rule or threshold35MIT OR Apache-2.0
rsomics-constraintBurt's structural-holes constraint — unweighted, value-exact port of networkx.constraint59MIT OR Apache-2.0
rsomics-cophenetCophenetic distances and cophenetic correlation coefficient from a hierarchical linkage matrix — value-exact vs…52MIT OR Apache-2.0
rsomics-core-numberK-core decomposition: compute the core number of every node in an undirected graph39MIT OR Apache-2.0
rsomics-correct-gc-biasCorrect the GC-content bias of a BAM into a coverage bedGraph, dividing each fragment by its computeGCBias R_gc factor — Rust…53MIT OR Apache-2.0
rsomics-correspondence-analysisCorrespondence Analysis (CA) of a non-negative feature/count table — scikit-bio skbio.stats.ordination.ca equivalent (chi-square…51MIT OR Apache-2.0
rsomics-count-matrixMerge multiple featureCounts/htseq-count outputs into a single gene × sample count matrix33MIT OR Apache-2.0
rsomics-coverage-coreGenome-binned BAM read-coverage primitive (deeptools countReadsPerBin port): per-bin read counts over a BGZF BAM via…163MIT OR Apache-2.0
rsomics-cpmCounts-per-million (CPM) and log2-CPM normalization of a gene count matrix, edgeR-compatible51MIT OR Apache-2.0
rsomics-cramervonmisesCramér-von Mises goodness-of-fit tests (one-sample + two-sample) — scipy.stats.cramervonmises / cramervonmises_2samp equivalent,…38MIT OR Apache-2.0
rsomics-csvioGo encoding/csv-exact CSV/TSV I/O for rsomics-tsv-* tools: a byte-faithful record writer and a strict-quote validator matching…144MIT OR Apache-2.0
rsomics-cuspCodon usage statistics table from nucleotide FASTA — EMBOSS cusp port13MIT OR Apache-2.0
rsomics-cut-treeCut a hierarchical linkage dendrogram into flat clusters — value-exact scipy.cluster.hierarchy.cut_tree reimplementation58MIT OR Apache-2.0
rsomics-dagDAG layer/depth analysis — value-exact port of networkx.topological_generations and dag_longest_path_length37MIT OR Apache-2.0
rsomics-de-volcanoAnnotate differential expression results with significance categories for volcano plots37MIT OR Apache-2.0
rsomics-debruijnde Bruijn graph types + linear-path collapse + unitig extraction for the rsomics-* tool family. Layer A primitive.21MIT OR Apache-2.0
rsomics-deletion-profilePer-base CIGAR-deletion rate along aligned reads — Rust port of RSeQC deletion_profile.py18MIT OR Apache-2.0
rsomics-derepFASTA dereplication — port of vsearch --derep_fulllength / --derep_prefix32MIT OR Apache-2.0
rsomics-derep-prefixPrefix FASTA dereplication — port of vsearch --derep_prefix14MIT OR Apache-2.0
rsomics-deseq-estimate-dispersionsDESeq2 estimateDispersions pipeline: median-of-ratios size factors, per-gene Cox-Reid NB-GLM dispersion (dispGeneEst), a…35MIT OR Apache-2.0
rsomics-deseq-fpkmDESeq2 fpkm(): median-of-ratios robust-normalized FPKM of a gene count matrix given per-gene basepair lengths36MIT OR Apache-2.0
rsomics-deseq-fpmDESeq2 fpm(): fragments per million of a gene count matrix, robust median-of-ratios library sizes (default) or raw column totals40MIT OR Apache-2.0
rsomics-deseq-lfc-shrinkDESeq2 lfcShrink(type="normal"): zero-centered normal-prior shrinkage of the log2 fold changes from a Wald-test fit…37MIT OR Apache-2.0
rsomics-deseq-lrtDESeq2 likelihood-ratio test (test=LRT): median-of-ratios normalization, MAP dispersion under the full design, NB-GLM fits of a…39MIT OR Apache-2.0
rsomics-deseq-norm-transformDESeq2 normTransform: log2(count / size-factor + 1) of a gene count matrix41MIT OR Apache-2.0
rsomics-deseq-prepFilter low-count genes and normalize a count matrix for differential expression — pre-DESeq2 prep41MIT OR Apache-2.0
rsomics-deseq-resultsDESeq2 nbinomWaldTest + results(): median-of-ratios normalization, MAP dispersion, NB-GLM Wald test of a two-group contrast with…35MIT OR Apache-2.0
rsomics-deseq-rlogDESeq2 rlog regularized-log transform of a gene count matrix37MIT OR Apache-2.0
rsomics-deseq-sizefactorsDESeq2 median-of-ratios size factors per sample from a gene count matrix38MIT OR Apache-2.0
rsomics-deseq-unmixDESeq2 unmix: deconvolve each sample into mixing proportions over pure cell-type signatures via per-sample box-constrained…14MIT OR Apache-2.0
rsomics-deseq-vstDESeq2 blind variance-stabilizing transform of a gene count matrix35MIT OR Apache-2.0
rsomics-detrendRemove a least-squares linear trend or the mean from a signal (scipy.signal.detrend equivalent)18MIT OR Apache-2.0
rsomics-differential-entropyDifferential (Shannon) entropy estimator from an i.i.d. sample — value-exact to scipy.stats.differential_entropy (vasicek / van…35MIT OR Apache-2.0
rsomics-digraph-metricsDirected-graph structural metrics (overall/node reciprocity, flow hierarchy) — value-exact port of networkx53MIT OR Apache-2.0
rsomics-digraph-propertiesDirected graph-property predicates (strongly/weakly-connected / aperiodic / semiconnected / dag) — value-exact port of networkx…53MIT OR Apache-2.0
rsomics-directed-componentsStrongly- and weakly-connected components of directed graphs — value-exact networkx equivalent (Tarjan SCC + BFS WCC)38MIT OR Apache-2.0
rsomics-dispersionBackstrom–Kleinberg dispersion (all-pairs) — value-exact Rust port of networkx nx.dispersion37MIT OR Apache-2.0
rsomics-distanceReading and validating scikit-bio-form square distance matrices (skbio DistanceMatrix invariants: unique IDs, hollow diagonal,…62MIT OR Apache-2.0
rsomics-dominanceGraph dominance analysis — immediate dominators + dominance frontiers of a directed graph. Value-exact port of…38MIT OR Apache-2.0
rsomics-dsspDSSP secondary-structure assignment from a PDB — Kabsch & Sander 8-state (H/B/E/G/I/T/S/-)57MIT OR Apache-2.0
rsomics-durbin-watsonDurbin-Watson autocorrelation statistic over a residual vector — statsmodels.stats.stattools.durbin_watson equivalent, value-exact18MIT OR Apache-2.0
rsomics-ebayes-corelimma-faithful empirical-Bayes moment estimation: fitFDist scaled-F prior estimator with digamma/trigamma/trigamma-inverse.37MIT OR Apache-2.0
rsomics-ecdfEmpirical CDF / survival function with Greenwood confidence intervals — value-exact to scipy.stats.ecdf for uncensored data21MIT OR Apache-2.0
rsomics-edge-betweennessEdge betweenness centrality for undirected graphs — value-exact networkx equivalent (Brandes 2008)54MIT OR Apache-2.0
rsomics-edge-filterClassic edge filters (Sobel, Scharr, Prewitt, Farid, Roberts) — value-exact port of scikit-image 0.2635MIT OR Apache-2.0
rsomics-edger-binom-testedgeR binomTest — per-gene two-sided exact binomial test of differential expression between two single libraries…49MIT OR Apache-2.0
rsomics-edger-cameraCAMERA competitive gene-set test accounting for inter-gene correlation (limma camera) — moderated-t z-scores, a…71MIT OR Apache-2.0
rsomics-edger-cpm-by-groupAverage CPM (or log2-CPM) per group via edgeR's negative-binomial one-group fit — Rust port of edgeR cpmByGroup75MIT OR Apache-2.0
rsomics-edger-diff-spliceedgeR diffSpliceDGE + topSpliceDGE — differential exon usage from a negative-binomial GLM fit (per-exon logFC/LR/p-value,…78MIT OR Apache-2.0
rsomics-edger-estimate-dispedgeR estimateDisp — negative-binomial common/trended/tagwise dispersion estimation by Cox-Reid adjusted profile likelihood +…54MIT OR Apache-2.0
rsomics-edger-exact-testedgeR exactTest — classic two-group negative-binomial exact test for differential expression (logFC, logCPM, PValue, FDR)53MIT OR Apache-2.0
rsomics-edger-glm-lrtedgeR glmFit + glmLRT — negative-binomial GLM fit and likelihood-ratio test of a coefficient or contrast (logFC, logCPM, LR,…54MIT OR Apache-2.0
rsomics-edger-glm-qlfedgeR glmQLFit + glmQLFTest — quasi-likelihood F-test for differential expression (logFC, logCPM, F, PValue, FDR)56MIT OR Apache-2.0
rsomics-edger-glm-treatedgeR glmTreat — negative-binomial GLM test of whether a coefficient/contrast log2-fold-change exceeds a threshold (logFC,…62MIT OR Apache-2.0
rsomics-edger-goodturingSimple Good-Turing frequency smoothing of count vectors/matrices into proportion estimates (incl. unseen-item mass) — Rust port…58MIT OR Apache-2.0
rsomics-edger-predfcedgeR predFC — predictive (prior-count-augmented) log2-fold-change coefficients from an NB-GLM fit, the shrunken logFC edgeR…50MIT OR Apache-2.0
rsomics-edger-rpkmLength-normalized expression (RPKM / log2-RPKM), overall and per-group — Rust port of edgeR rpkm + rpkmByGroup55MIT OR Apache-2.0
rsomics-effective-sizeBurt's structural-holes effective size per node — unweighted undirected graph, Borgatti simplified formula35MIT OR Apache-2.0
rsomics-ehh-decaySingle-locus EHH (extended haplotype homozygosity) decay profile around a focal SNP from a phased VCF, value-exact to…39MIT OR Apache-2.0
rsomics-eigenvector-centralityEigenvector centrality of undirected graphs (power-iteration, value-exact vs networkx)53MIT OR Apache-2.0
rsomics-energy-distance1-D energy distance between two empirical distributions — scipy.stats.energy_distance equivalent, value-exact19MIT OR Apache-2.0
rsomics-entropyShannon entropy and Kullback-Leibler divergence of a discrete distribution — value-exact to scipy.stats.entropy37MIT OR Apache-2.0
rsomics-epps-singletonEpps-Singleton two-sample test on the empirical characteristic function — scipy.stats.epps_singleton_2samp value-exact49MIT OR Apache-2.0
rsomics-equalize-histHistogram equalization for bioimaging arrays — value-exact port of skimage.exposure.equalize_hist59MIT OR Apache-2.0
rsomics-f-onewayOne-way ANOVA F-test (scipy.stats.f_oneway equivalent) — value-exact F statistic and Cephes-incbet F-distribution p-value, faster…19MIT OR Apache-2.0
rsomics-faith-pdPer-sample Faith's phylogenetic diversity (PD) from a feature count table + a Newick tree — scikit-bio faith_pd equivalent,…52MIT OR Apache-2.0
rsomics-fasta-ampliconExtract amplicons from FASTA/FASTQ via a primer pair — seqkit amplicon port92MIT OR Apache-2.0
rsomics-fasta-countCount sequences in FASTA files (gz-transparent)16MIT OR Apache-2.0
rsomics-fasta-digestIn-silico protein digestion — trypsin/LysC/other enzymes, missed cleavages, peptide mass filter70MIT OR Apache-2.0
rsomics-fasta-filterFilter FASTA sequences by length — seqkit seq -m equivalent16MIT OR Apache-2.0
rsomics-fasta-fx2tabConvert FASTA/Q to tabular form with computed per-record columns (length, GC, GC-skew, avg-qual, base content/count, alphabet,…82MIT OR Apache-2.0
rsomics-fasta-grepFilter FASTA records by name regex — seqkit grep equivalent for FASTA16MIT OR Apache-2.0
rsomics-fasta-headOutput the first N FASTA records — seqkit head equivalent for FASTA16MIT OR Apache-2.0
rsomics-fasta-indexFASTA index (.fai) creation, random-access fetch, and sequence dictionary — Rust port of samtools faidx/dict123MIT OR Apache-2.0
rsomics-fasta-locateLocate subsequences/motifs in FASTA files — seqkit locate port142MIT OR Apache-2.0
rsomics-fasta-maskMask FASTA sequences by BED regions — soft-mask (lowercase) or hard-mask (N)67MIT OR Apache-2.0
rsomics-fasta-n50Compute N50, L50, and assembly statistics from FASTA106MIT OR Apache-2.0
rsomics-fasta-orfFind and extract open reading frames from nucleotide FASTA — EMBOSS getorf port13MIT OR Apache-2.0
rsomics-fasta-renameRename FASTA sequence IDs with sequential numbering17MIT OR Apache-2.0
rsomics-fasta-sampleRandom subsample of FASTA sequences — seqkit sample for FASTA17MIT OR Apache-2.0
rsomics-fasta-slidingSliding-window subsequence extraction from FASTA — seqkit sliding port103MIT OR Apache-2.0
rsomics-fasta-sortSort FASTA sequences by name or length — seqkit sort equivalent16MIT OR Apache-2.0
rsomics-fasta-statsPer-record statistics for FASTA files (num_seqs, sum_len, GC%, N50, …) — Rust port of `seqkit stats` (FASTA-only subset).205MIT OR Apache-2.0
rsomics-fasta-subseqExtract FASTA subsequences by 1-based region — seqkit subseq port96MIT OR Apache-2.0
rsomics-fasta-translateTranslate DNA/RNA FASTA to protein sequences (six-frame)93MIT OR Apache-2.0
rsomics-fasta-upperUppercase FASTA sequences16MIT OR Apache-2.0
rsomics-fasta-utilsFASTA utility toolkit — count, chroms, len, revcomp, rename, tab, wrap, unique, convert, and more90MIT OR Apache-2.0
rsomics-fasta-validateValidate FASTA format integrity60MIT OR Apache-2.0
rsomics-fastpFast FASTQ quality control and preprocessing46MIT OR Apache-2.0
rsomics-fastq-complexityFASTQ low-complexity filter — discard reads whose per-base change fraction falls below a threshold38MIT OR Apache-2.0
rsomics-fastq-correctFASTQ k-mer-spectrum substitution-error correction. Independent Rust port of BFC (lh3): trusted-k-mer threshold + best-first…41MIT OR Apache-2.0
rsomics-fastq-dedupSequence-based FASTQ deduplication (kmer-bin or full-sequence hash). Rust port consolidating fastp -D and seqkit rmdup.60MIT OR Apache-2.0
rsomics-fastq-downsampleDeterministic random downsampling of FASTQ to a target read count or fraction66MIT OR Apache-2.0
rsomics-fastq-filterFASTQ per-read quality + length filter. Rust port of fastp's quality/length filter (pass/fail whole reads; no trimming). SE and…71MIT OR Apache-2.0
rsomics-fastq-grepFilter FASTQ records by read name pattern — seqkit grep equivalent16MIT OR Apache-2.0
rsomics-fastq-lenOutput per-read lengths from FASTQ — for read-length distribution QC16MIT OR Apache-2.0
rsomics-fastq-mergeMerge overlapping paired-end FASTQ reads into consensus reads — Rust port of fastp's overlap merge (+ optional overlap base…57MIT OR Apache-2.0
rsomics-fastq-pairRe-pair shuffled paired-end FASTQ reads by name68MIT OR Apache-2.0
rsomics-fastq-qualityFASTQ sliding-window and leading/trailing quality trimmer — Rust port of fastp/Trimmomatic quality-trim algorithms58MIT OR Apache-2.0
rsomics-fastq-sampleRandom subsample FASTQ records by fraction or exact count — seqkit sample / seqtk sample equivalent83MIT OR Apache-2.0
rsomics-fastq-splitSplit a FASTQ into N files or by line count. Rust port of fastp's split (deterministic --split_by_lines is byte-equal to fastp…39MIT OR Apache-2.0
rsomics-fastq-statsPer-file statistics for FASTQ files (num_seqs, sum_len, N50, GC%, Q20/Q30%, AvgQual, …) — Rust port of `seqkit stats` (FASTQ).68MIT OR Apache-2.0
rsomics-fastq-to-fastaConvert FASTQ to FASTA (strip quality lines) — seqkit fq2fa equivalent16MIT OR Apache-2.0