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* biology/bcf-score: Bcftools plugins for GWAS-VCF summary statisticsJason W. Bacon2023-02-251-0/+1
| | | | | | Score is a set of tools in the form of a bcftools plugin, for handling and converting summary statistics files following the GWAS-VCF specification.
* biology/wfa2-lib: Exact gap-affine algorithm using homologyJason W. Bacon2023-01-301-0/+1
| | | | | | | | | | | | The wavefront alignment (WFA) algorithm is an exact gap-affine algorithm that takes advantage of homologous regions between the sequences to accelerate the alignment process. Unlike traditional dynamic programming algorithms that run in quadratic time, the WFA runs in time O(ns+s^2), proportional to the sequence length n and the alignment score s, using O(s^2) memory (or O(s) using the ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple computational patterns that the modern compilers can automatically vectorize for different architectures without adapting the code.
* biology/atac-seq: Metaport for ATAC-Seq analysisJason W. Bacon2023-01-111-0/+1
| | | | | Metaport to install tools for typical ATAC-Seq analysis, including QC, adapter trimming, alignment, and differential analysis.
* biology/py-biosig: New port: Library for reading and writing different ↵Yuri Victorovich2022-12-301-0/+1
| | | | biosignal data format
* biology/rna-seq: Metaport for RNA-Seq analysisJason W. Bacon2022-12-121-0/+1
| | | | | Metaport to install tools for typical RNA-Seq analysis, including QC, adapter trimming, alignment, and differential analysis.
* biology/fasda: Fast and simple differential analysisJason W. Bacon2022-12-121-0/+1
| | | | | | | | FASDA aims to provide a fast and simple differential analysis tool that just works and does not require any knowledge beyond basic Unix command-line skills. The code is written entirely in C to maximize efficiency and portability, and to provide a simple command-line user interface.
* biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder ↵Yuri Victorovich2022-12-061-0/+1
| | | | for genomes and metagenomes
* biology/metaeuk: New port: Gene discovery and annotation for large-scale ↵Yuri Victorovich2022-11-261-0/+1
| | | | eukaryotic metagenomics
* biology/augustus: New port: Genome annotation toolYuri Victorovich2022-11-251-0/+1
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* biology/barrnap: New port: BAsic Rapid Ribosomal RNA PredictorYuri Victorovich2022-11-251-0/+1
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* biology/megahit: Ultra-fast single-node metagenomics assemblyJason W. Bacon2022-11-221-0/+1
| | | | | | | MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction.
* biology/libcombine: New port: C++ library for working with the COMBINE ↵Yuri Victorovich2022-10-211-0/+1
| | | | archive format
* biology/py-valerius: New port: Python bioinformatics toolsYuri Victorovich2022-10-041-0/+1
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* biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale ↵Yuri Victorovich2022-08-071-0/+1
| | | | genome searching
* biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-toolsYuri Victorovich2022-07-071-0/+1
| | | | | | | | This reverts commit 1cb8897f610a381ddf2802eb09acfba97b15b505. sra-tools needs to be updated first. Reported by: Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@
* biology/ngs-sdk: Remove, ngs was moved into sra-toolsYuri Victorovich2022-07-061-1/+0
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* biology/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take ↵Yuri Victorovich2022-06-191-1/+0
| | | | maintainership
* biology/py-mrcfile: New port: MRC file I/O library which is used in ↵Yuri Victorovich2022-05-011-0/+1
| | | | structural biology
* biology/fastq-trim: Lightening fast sequence read trimmerJason W. Bacon2022-03-191-0/+1
| | | | | Fastq-trim is a lightening fast read trimming tool for QA of DNA and RNA reads prior to analyses such as RNA-Seq.
* biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)Jason W. Bacon2022-02-031-0/+2
| | | | | | Read and write Generic Feature Format (GFF) with Biopython integration. Also adding py-dna-features-viewer to Makefile, missed on last commit
* biology/libgff: GFF/GTF parsing library based on GCLibJason W. Bacon2021-12-051-0/+1
| | | | | | | | | | | | This is an attempt to perform a simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase. There are not many (any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, and the goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn. Note: This library draws directly from the code in GFFRead and GCLib, and exists primarily to remove functionality (and hence code) that is unnecessary for our downstream purposes. In the future, it may be appropriate to just replace this library wholesale with GCLib.
* biology/bio-mocha: bcftools plugin for mosaic chromosomal alterationsJason W. Bacon2021-12-031-0/+1
| | | | | | | | | MoChA is a bcftools plugin released under the MIT license for mosaic chromosomal alteration detection and analysis from DNA microarray or whole genome sequence data. It can be used both with Illumina and Affymetrix data. It can also be used for detection of germline copy number variants. Data can be prepared in usable file formats using the gtc2vcf plugin.
* biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etcJason W. Bacon2021-11-101-0/+1
| | | | | GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more.
* */Makefile: Sort SUBDIRsPo-Chuan Hsieh2021-10-251-1/+1
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* biology/py-deeptools: User-friendly tools for exploring deep-sequencing dataJason W. Bacon2021-10-141-0/+1
| | | | | | | | | | deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
* biology/py-bigwig: Rename to biology/py-pybigwigJason W. Bacon2021-10-131-1/+1
| | | | Fully match upstream name
* biology/py-pybigwig: remove, duplicate of biology/py-bigwigAntoine Brodin2021-10-131-1/+0
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* biology/py-pybigwig: Fix poudriere buildJason W. Bacon2021-10-131-0/+1
| | | | Typo in post-install
* biology/py-pybigwig: Python access to bigWig files using libBigWigJason W. Bacon2021-10-131-0/+1
| | | | | | py-bigwig is a python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. This extension uses libBigWig for local and remote file access.
* biology/py-py2bit: Python interface for 2bit packed nucleotide filesJason W. Bacon2021-10-131-0/+1
| | | | | | py2bit is a python extension, written in C, for quick access to 2bit files for randomly accessible, packed nucleotide sequences. The extension uses lib2bit for file access.
* biology/bamutil: Utilities for working with SAM/BAM filesJason W. Bacon2021-10-121-0/+1
| | | | | | | Utilities for working on SAM/BAM files from The Center for Statistical Genetics at the University of Michigan School of Public Health. It includes numerous functions such as splitting, merging, trimming reads, filtering, validation, diff, etc.
* biology/libneurosim: New port: Common interfaces for neuronal simulatorsYuri Victorovich2021-10-081-0/+1
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* */Makefile: Sort SUBDIRsPo-Chuan Hsieh2021-09-211-2/+2
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* biology/py-libsedml: New port: SED-ML library for PythonYuri Victorovich2021-09-191-0/+1
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* biology/libsedml: New port: C++ SED-ML libraryYuri Victorovich2021-09-191-0/+1
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* biology/py-libnuml: New port: Numerical Markup Language for PythonYuri Victorovich2021-09-191-0/+1
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* biology/libnuml: New port: C++ library for Numerical Markup LanguageYuri Victorovich2021-09-191-0/+1
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* biology/sam2pairwise: Show pairwise alignment for each read in a SAM fileJason W. Bacon2021-09-071-0/+1
| | | | | sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.
* biology/py-pywgsim: Modified wgsim genomic data simulatorJason W. Bacon2021-09-061-0/+1
| | | | | | pywgsim is a modified version of the wgsim short read simulator. The code for wgsim has been modified to allow visualizing the simulated mutations as a GFF file.
* biology/biolibc-tools: High-performance tools based on biolibcJason W. Bacon2021-08-301-0/+1
| | | | | | | Biolibc-tools is a collection of simple fast, memory-efficient, programs for processing biological data. These are simple programs built on biolibc that are not complex enough to warrant a separate project.
* biology/bfc: Correct sequencing errors from Illumina sequencing dataJason W. Bacon2021-08-231-0/+1
| | | | | | | BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes.
* biology/flash: Fast Length Adjustment of SHort readsJason W. Bacon2021-08-231-0/+1
| | | | | | | | | | FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
* biology/py-PySCeS: New port: Python Simulator for Cellular SystemsYuri Victorovich2021-08-171-0/+1
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* biology/py-python-libsbml: New port: LibSBML Python APIYuri Victorovich2021-08-171-0/+1
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* biology/sigviewer: New port: Viewing application for biosignalsYuri Victorovich2021-08-171-0/+1
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* biology/biosig: New port: Library for reading and writing different ↵Yuri Victorovich2021-08-171-0/+1
| | | | biosignal data format
* biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 filesJason W. Bacon2021-08-131-0/+1
| | | | | | | | | | The ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format. It provides: o Implementation of the fast5 file schema using h5py library o Methods to interact with and reflect the fast5 file schema o Tools to convert between multi_read and single_read formats o Tools to compress/decompress raw data in files
* biology/erminej: Analyses of gene sets, e.g. gene expression profilingJason W. Bacon2021-07-091-0/+1
| | | | | | | | | | ErmineJ performs analyses of gene sets in high-throughput genomics data such as gene expression profiling studies. A typical goal is to determine whether particular biological pathways are "doing something interesting" in an experiment that generates long lists of candidates. The software is designed to be used by biologists with little or no informatics background (but if you do, you might be interested in the CLI or the R support).
* biology/py-goatools: Tools for processing and visualizing Gene Ontology termsJason W. Bacon2021-07-021-0/+1
| | | | | Goatools is a python library for processing Gene Ontology (GO) terms. It includes routines for processing, filtering, and visualizing GO data.
* biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suiteJason W. Bacon2021-06-241-0/+1
| | | | | | | | | | | MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.
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