fastreeR - Phylogenetic, Distance and Other Calculations on VCF and Fasta Files
Calculate distances, build phylogenetic trees or perform hierarchical clustering between the samples of a VCF or FASTA file. Functions are implemented in Java-11 and called via rJava. Parallel implementation that operates directly on the VCF or FASTA file for fast execution.
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phylogeneticsmetagenomicsclusteringopenjdk
6.64 score 31 stars 28 scripts 344 downloads
jvecfor - Fast K-Nearest Neighbor Search for Single-Cell Analysis
Drop-in replacement for BiocNeighbors::findKNN using the jvecfor Java library, which builds on the jvector library to leverage the Java Vector API for portable SIMD acceleration across AVX2, AVX-512, and ARM NEON hardware. jvecfor/jvector implements HNSW-DiskANN approximate search and VP-tree exact search. The package achieves approximately 2x speedup over Annoy-based search at n >= 50K cells while returning output structurally identical to BiocNeighbors, making it suitable for seamless integration into existing Bioconductor single-cell workflows. Convenience wrappers delegate shared nearest-neighbor (SNN) and k-nearest-neighbor (KNN) graph construction to the bluster package.
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singlecellgraphandnetworkclusteringclassification
5.02 score 3 stars 6 scripts 278 downloadsmetabinR - Abundance and Compositional Based Binning of Metagenomes
Provide functions for performing abundance and compositional based binning on metagenomic samples, directly from FASTA or FASTQ files. Functions are implemented in Java and called via rJava. Parallel implementation that operates directly on input FASTA/FASTQ files for fast execution. Inputs may be file paths or Biostrings/ShortRead sequence objects; results are returned as a MetabinResult S4 object wrapping cluster assignments, algorithm parameters, and input metadata.
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classificationclusteringmicrobiomesequencingsoftwareopenjdk
4.48 score 2 stars 4 scripts 352 downloadspanpathAudit - Audit Sequence Preservation in GFA Traversals
Audits source FASTA sequences against named paths and coordinate-aware walks in GFA files. It reports exact recovery, divergence coordinates, digests, and optional base-level statistics. Graph topology is not validated.
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alignmentdataimportgenomeassemblygeneticssequencingzlibcpp
3.00 score