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ntw44/cgit/cgit.cgi/freebsd-ports-gnome/commit/biology/Makefile?id=ab50f8435a78a574ac5ce683004b078c5baf209d'>biology/ncbi-entrez-direct: Access to the NCBI's interconnected databasesJason W. Bacon2021-04-251-0/+1 * New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and R...Yuri Victorovich2021-04-201-0/+1 * biology/snpeff: Genetic variant annotation and effect prediction toolboxJason W. Bacon2021-04-191-0/+1 * biology/bbmap: BBMap short read aligner, and other bioinformatic toolsJason W. Bacon2021-04-191-0/+1 * biology/readseq: Read and reformat biosequences, Java command-line versionJason W. Bacon2021-04-181-0/+1 * New port: biology/seqkit: Cross-platform and ultrafast toolkit for FASTA/Q fi...Yuri Victorovich2021-04-171-0/+1 * biology/py-crossmap: Lift over genomics coordinates between assembliesJason W. Bacon2021-04-131-0/+1 * biology/py-bigwig: Python access to bigWig files using libBigWigJason W. Bacon2021-04-131-0/+1 * New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequenc...Yuri Victorovich2021-04-121-0/+1 * Remove expired ports:Rene Ladan2021-04-081-3/+0 * One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0 * Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-2/+0 * biology/vcf2hap: Generate .hap file from VCF for haplohseqJason W. Bacon2021-03-241-0/+1 * biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF fileJason W. Bacon2021-03-231-0/+1 * biology/vcf-split: Split a multi-sample VCF into single-sample VCFsJason W. Bacon2021-03-211-0/+1 * biology/biolibc: Low-level high-performance bioinformatics libraryJason W. Bacon2021-03-211-0/+1 * biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF formatJason W. Bacon2021-03-161-0/+1 * Move: biology/py-fastTSNE -> math/py-openTSNEYuri Victorovich2021-03-141-1/+0 * New port: biology/rampler: Standalone module for sampling genomic sequencesYuri Victorovich2021-01-191-0/+1 * New port: biology/edlib: Fast C++ library for sequence alignment using edit d...Yuri Victorovich2021-01-191-0/+1 * New port: biology/spoa: C++ implementation of the partial order alignment (PO...Yuri Victorovich2021-01-191-0/+1 * New port: biology/biosoup: Collection of C++ header-only data structures for ...Yuri Victorovich2021-01-191-0/+1 * New port: biology/bioparser: C++ header only parsing library for several form...Yuri Victorovich2021-01-191-0/+1 * Hook haplohseq to the buildAntoine Brodin2021-01-151-0/+1 * biology/pooler: Optimise DNA sequencing primer-set combinationsJason W. Bacon2020-11-161-0/+1 * biology/py-biom-format: Restore in preparation for an update to v2.1.8Joseph Mingrone2020-09-251-0/+1 * Remove expired ports:Rene Ladan2020-09-191-2/+0 * Remove expired ports:Rene Ladan2020-08-271-1/+0 * Remove deprecated ports:Rene Ladan2020-08-151-1/+0 * Add rubygem-bio-shell 1.0.0Sunpoet Po-Chuan Hsieh2020-07-241-0/+1 * Add rubygem-bio-old-biofetch-emulator 1.0.0Sunpoet Po-Chuan Hsieh2020-07-241-0/+1 * Add rubygem-bio-executables 1.0.0Sunpoet Po-Chuan Hsieh2020-07-241-0/+1 * biology/picard-tools: CLI tools for manipulating sequencing dataJason W. Bacon2020-06-131-0/+1 * biology/bioawk: BWK awk modified for biological dataJason W. Bacon2020-06-051-0/+1 * biology/subread: Read alignment, quantification and mutation discoveryJason W. Bacon2020-06-051-0/+1 * bioloty/vt: Discovers short variants from Next Generation Sequencing dataJason W. Bacon2020-06-051-0/+1 * New port: biology/py-hits: Utilities for processing high-throughput sequencin...Yuri Victorovich2020-05-161-0/+1 * New port: biology/py-scikit-bio: Data structures, algorithms, educational res...Yuri Victorovich2020-05-161-0/+1 * New port: biology/py-pandas-charm: Library for getting character matrices int...Yuri Victorovich2020-05-161-0/+1 * New port: biology/py-ete3: Framework for the analysis and visualization of treesYuri Victorovich2020-05-161-0/+1 * New port: biology/scrm: Coalescent simulator for biological sequencesYuri Victorovich2020-05-151-0/+1 * - Resurrect and unbreak by updating to version 34.0Alexey Dokuchaev2020-05-101-0/+1 * Remove expired ports:Rene Ladan2020-05-051-5/+0 * biology/plink: Whole genome association analysis toolsetJason W. Bacon2020-05-051-0/+1 * biology/gcta: Genome-wide Complex Trait AnalysisJason W. Bacon2020-04-151-0/+1 * Resurrect biology/linux-foldingathomeMateusz Piotrowski2020-03-221-0/+1 * Remove expired ports:Rene Ladan2020-01-271-2/+0 * Add p5-Bio-Variation 1.7.4Sunpoet Po-Chuan Hsieh2019-12-091-0/+1 * Add p5-Bio-DB-NCBIHelper 1.7.6Sunpoet Po-Chuan Hsieh2019-12-091-0/+1 * Add p5-Bio-DB-EMBL 1.7.4Sunpoet Po-Chuan Hsieh2019-12-091-0/+1 * Remove expired ports:Rene Ladan2019-10-161-2/+0 * biology/tophat: Fast splice junction mapper for RNA-Seq readsJason W. Bacon2019-09-271-0/+1 * biology/py-multiqc: Aggregate bioinformatics analysis reportsJason W. Bacon2019-09-241-0/+1 * biology/haplohseq: Identify regions of allelic imbalanceJason W. Bacon2019-09-161-0/+1 * New port: biology/libbigwig: C library for handling bigWig files (containing ...Yuri Victorovich2019-07-121-0/+1 * New port: biology/viennarna: Alignment tools for the structural analysis of RNAYuri Victorovich2019-06-241-0/+1 * New port: biology/treekin: Efficient computation of RNA folding dynamicsYuri Victorovich2019-06-161-0/+1 * biology/bolt-lmm: Mixed model association testing and variance component anal...Jason W. Bacon2019-05-261-0/+1 * New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their...Yuri Victorovich2019-05-261-0/+1 * New port: biology/mothur: Software for bioinformatics of the microbial ecolog...Yuri Victorovich2019-05-211-0/+1 * New port: biology/hhsuite: Remote protein homology detection suiteYuri Victorovich2019-05-191-0/+1 * biology/gemma: Genome-wide Efficient Mixed Model AssociationJason W. Bacon2019-05-171-0/+1 * biology/vsearch: Versatile open-source tool for metagenomicsJason W. Bacon2019-05-101-0/+1 * biology/fastp: Ultra-fast all-in-one FASTQ preprocessorJason W. Bacon2019-05-031-0/+1 * biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequencesJason W. Bacon2019-04-251-0/+1 * biology/star: Spliced Transcripts Alignment to a ReferenceJason W. Bacon2019-04-221-0/+1 * New port: biology/py-xenaPython: API for Xena Hub to access genetic informati...Yuri Victorovich2019-04-131-0/+1 * biology/py-dnaio: Read and write FASTQ and FASTAJason W. Bacon2019-03-251-0/+1 * Qt4 deprecation: Remove Qt4 and its consumes.Tobias C. Berner2019-03-171-1/+0 * New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end se...Yuri Victorovich2019-02-251-0/+1 * Add p5-Bio-Cluster 1.7.3Sunpoet Po-Chuan Hsieh2019-02-211-0/+1 * New port: biology/figtree: Graphical viewer of phylogenetic treesYuri Victorovich2019-02-041-0/+1 * New port: biology/graphlan: High-quality circular representations of taxonomi...Yuri Victorovich2019-02-041-0/+1 * New port: biology/prodigy-lig: Prediction of protein-small molecule binding a...Yuri Victorovich2019-02-041-0/+1 * New port: biology/prodigal: Protein-coding gene prediction for prokaryotic ge...Yuri Victorovich2019-02-041-0/+1 * New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein descripti...Yuri Victorovich2019-01-291-0/+1 * Sort categories Makefiles.Mathieu Arnold2019-01-231-1/+1 * New port: biology/hisat2: Program for mapping next-generation sequencing readsJason W. Bacon2019-01-121-0/+1 * Remove expired ports:Rene Ladan2018-12-211-1/+0 * New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNEYuri Victorovich2018-12-151-0/+1 * Remove biology/njplotJoseph Mingrone2018-12-111-1/+0 * New port: math/checkm: Quality assessment tool for the microbial genomesYuri Victorovich2018-12-071-0/+1 * New port: math/groopm: Metagenomic binning suiteYuri Victorovich2018-12-071-0/+1 * New port: biology/gatk: Variant discovery in high-throughput sequencing dataYuri Victorovich2018-12-031-0/+1 * New port: biology/py-gffutils: Work with GFF and GTF files in a flexible data...Yuri Victorovich2018-10-191-0/+1 * New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subse...Yuri Victorovich2018-10-191-0/+1 * New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) f...Yuri Victorovich2018-10-191-0/+1 * New port: biology/ncbi-cxx-toolkit: NCBI C++ ToolkitYuri Victorovich2018-10-081-0/+1 * biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/Yuri Victorovich2018-10-071-1/+0 * New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq dataYuri Victorovich2018-09-211-0/+1 * Remove expired ports:Rene Ladan2018-08-171-1/+0 * Regular sorting of categories Makefiles.Mathieu Arnold2018-08-081-1/+1 * New port: biology/py-orange3-single-cell: Orange add-on for gene expression o...Yuri Victorovich2018-08-071-0/+1 * New port: biology/exonerate: Generic tool for sequence alignmentYuri Victorovich2018-07-131-0/+1 * New port: biology/stringtie: Transcript assembly and quantification for RNA-seqYuri Victorovich2018-07-121-0/+1 * New port: biology/cytoscape: Software to visualize molecular interaction netw...Yuri Victorovich2018-07-031-0/+1 * New port: biology/igv: Visualization tool for genomic datasetsYuri Victorovich2018-06-261-0/+1 * New port: biology/py-orange3-bioinformatics: Orange add-on providing common f...Yuri Victorovich2018-06-141-0/+1 * New port: biology/py-Genesis-PyAPI: API for the Genesis platform for genetics...Yuri Victorovich2018-06-131-0/+1 * New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Se...Yuri Victorovich2018-06-111-0/+1 * Remove expired ports:Rene Ladan2018-06-071-4/+0 * Add new port: biology/infernalKirill Ponomarev2018-06-061-0/+1 * biology/clustal-omega: Multiple alignment of nucleic acid and protein, replac...Jason W. Bacon2018-05-221-0/+1 * biology/clustalx: Multiple alignment of nucleic acid and protein sequences wi...Jason W. Bacon2018-05-221-0/+1 * New port, biology/hyphy: Hypothesis testing using PhylogeniesJoseph Mingrone2018-05-111-0/+1 * biology/unanimity: Pacific Biosciences consensus library and applicationsJason W. Bacon2018-04-241-0/+1 * biology/pbcopper: Core C++ library for Pacific Biosciences toolsJason W. Bacon2018-04-241-0/+1 * biology/pbbam: PacBio BAM C++ library, with SWIG bindingsJason W. Bacon2018-04-241-0/+1 * biology/pbseqan: Pacific Biosciences patched and stripped down SeqAnJason W. Bacon2018-04-221-0/+1 * biology/ddocent: Bash pipeline for RAD sequencingJason W. Bacon2018-04-201-0/+1 * biology/freebayes: Bayesian haplotype-based polymorphism discovery and genoty...Jason W. Bacon2018-04-201-0/+1 * biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF filesJason W. Bacon2018-04-171-0/+1 * biology/fastahack: Utility for indexing and sequence extraction from FASTA filesJason W. Bacon2018-04-161-0/+1 * biology/smithwaterman: Smith-waterman-gotoh alignment algorithmJason W. Bacon2018-04-161-0/+1 * biology/tabixpp: C++ wrapper to tabix indexerJason W. Bacon2018-04-151-0/+1 * biology/pear-merger: Memory-efficient and accurate paired-end read mergerJason W. Bacon2018-04-051-0/+1 * biology/seqtk: Tool for processing sequences in FASTA/FASTQ formatJason W. Bacon2018-04-041-0/+1 * biology/trimadap: Trim adapter sequences from Illumina dataJason W. Bacon2018-04-041-0/+1 * biology/rainbow: Efficient clustering and assembling of short readsJason W. Bacon2018-04-031-0/+1 * biology/stacks: Software pipeline for building loci from short-read sequencesJason W. Bacon2018-03-311-0/+1 * biology/bamtools: API and toolkit for handling BAM filesJason W. Bacon2018-03-28