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Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
This package provides a fast structural variation caller for long-read sequencing data.
Fast and flexible inference of the distribution of fitness effects (DFE), VCF-SFS parsing with ancestral allele and site-degeneracy annotation.
Fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool has multi-threading support to afford high performance.
Expected Genettic Relationship Matrix computation
SFS parsing with site filtration and annotation, from VCF, Zarr, or tree sequences.
FastDup is a tool designed to locate and tag duplicate reads in a coordinate-sorted SAM or BAM file. It uses the same core algorithm as Picard MarkDuplicates to produce identical results and utilizes spdlog for logging, with the default level set to 'info'.
This package provides Site frequency spectrum estimation based on window expectation-maximisation algorithm.
Smart and Accurate Polishing of Phased Haplotypes Integrating Read Enhancements (SAPPHIRE)
R package for wavelet variance and correlation decompositions of genomic signals, averaging across chromosomes (or more generally any set of multiple temporal or spatial signals).
Inference of ploidy and heterozygosity structure using whole genome sequencing data.
Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Reference-free profiling of polyploid genomes.
Expected Genettic Relationship Matrix computation
SHAPEIT5 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and sequencing data.
A fast K-mer counter for high-fidelity shotgun datasets.
GCTA (Genome-wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been greatly extended for many other analyses of data from genome-wide association studies (GWASs).
phase genomic variants using DNA sequencing reads.
Python bindings to spoa.
Minibwa aligns short reads against a reference genome. It is the successor of bwa-mem with a different algorithm. Minibwa is over three times as fast as the original bwa-mem and twice as fast as bwa-mem2 at comparable accuracy. While minibwa works with accurate long reads, minimap2 is more robust under high error rate.
A hidden Markov model approach for simultaneously estimating local ancestry and admixture time using next generation sequence data in samples of arbitrary ploidy.
This package provides Site frequency spectrum estimation based on window expectation-maximisation algorithm.
This package provides Bindings to libdeflate for DEFLATE (de)compression exposed as non-streaming buffer operations. Contains bindings for raw deflate, zlib, and gzip data.