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Number of commits found: 309 (showing only 100 on this page)

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Sat, 25 Feb 2023
[ 14:27 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:68c12d4ad402d885c078499f05c4a3919276398b  commit hash:68c12d4ad402d885c078499f05c4a3919276398b  commit hash:68c12d4ad402d885c078499f05c4a3919276398b  68c12d4 
biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics

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.
Mon, 30 Jan 2023
[ 19:09 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:595d0dabcfdc4e4a2eefbfff154f7c2ab04488be  commit hash:595d0dabcfdc4e4a2eefbfff154f7c2ab04488be  commit hash:595d0dabcfdc4e4a2eefbfff154f7c2ab04488be  595d0da 
biology/wfa2-lib: Exact gap-affine algorithm using homology

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.
Wed, 11 Jan 2023
[ 23:47 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf  commit hash:d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf  commit hash:d2c13cc6fdc1acf4009e477d00ec09b03ff2bacf  d2c13cc 
biology/atac-seq: Metaport for ATAC-Seq analysis

Metaport to install tools for typical ATAC-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
Fri, 30 Dec 2022
[ 08:32 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:8ce2f7242767fa9f76b45f930aa586c1852f7800  commit hash:8ce2f7242767fa9f76b45f930aa586c1852f7800  commit hash:8ce2f7242767fa9f76b45f930aa586c1852f7800  8ce2f72 
biology/py-biosig: New port: Library for reading and writing different biosignal
data format
Mon, 12 Dec 2022
[ 17:30 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22  commit hash:8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22  commit hash:8e926be18e0ab02a6d7ac35958a2eb6f0bee5a22  8e926be 
biology/rna-seq: Metaport for RNA-Seq analysis

Metaport to install tools for typical RNA-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.
[ 17:17 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:455ea913be3f86da7096e18368b4ac62e319dbe5  commit hash:455ea913be3f86da7096e18368b4ac62e319dbe5  commit hash:455ea913be3f86da7096e18368b4ac62e319dbe5  455ea91 
biology/fasda: Fast and simple differential analysis

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.
Tue, 6 Dec 2022
[ 15:41 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:29c79a3b6aee93dbe5b65e863bcb33e1bb773276  commit hash:29c79a3b6aee93dbe5b65e863bcb33e1bb773276  commit hash:29c79a3b6aee93dbe5b65e863bcb33e1bb773276  29c79a3 
biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for
genomes and metagenomes
Sat, 26 Nov 2022
[ 11:04 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:affc6502d525205e07e5770118a8dc8577bb7d1d  commit hash:affc6502d525205e07e5770118a8dc8577bb7d1d  commit hash:affc6502d525205e07e5770118a8dc8577bb7d1d  affc650 
biology/metaeuk: New port: Gene discovery and annotation for large-scale
eukaryotic metagenomics
Fri, 25 Nov 2022
[ 23:55 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:8b43ef57fd38af532b6619eaade5b35b053b4afd  commit hash:8b43ef57fd38af532b6619eaade5b35b053b4afd  commit hash:8b43ef57fd38af532b6619eaade5b35b053b4afd  8b43ef5 
biology/augustus: New port: Genome annotation tool
[ 03:08 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:a7eec55e9ca07d154f1de127c3ecc6187bce06d6  commit hash:a7eec55e9ca07d154f1de127c3ecc6187bce06d6  commit hash:a7eec55e9ca07d154f1de127c3ecc6187bce06d6  a7eec55 
biology/barrnap: New port: BAsic Rapid Ribosomal RNA Predictor
Tue, 22 Nov 2022
[ 16:39 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:acb3a0de6468b1fe930e53af1894505e9b8d64c7  commit hash:acb3a0de6468b1fe930e53af1894505e9b8d64c7  commit hash:acb3a0de6468b1fe930e53af1894505e9b8d64c7  acb3a0d 
biology/megahit: Ultra-fast single-node metagenomics assembly

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.
Fri, 21 Oct 2022
[ 07:05 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:47f90fecad58186514d8c977f75c2db2c5252e35  commit hash:47f90fecad58186514d8c977f75c2db2c5252e35  commit hash:47f90fecad58186514d8c977f75c2db2c5252e35  47f90fe 
biology/libcombine: New port: C++ library for working with the COMBINE archive
format
Tue, 4 Oct 2022
[ 04:06 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:f83007151dea80e9f9cf09909f95ff4ea1cbab36  commit hash:f83007151dea80e9f9cf09909f95ff4ea1cbab36  commit hash:f83007151dea80e9f9cf09909f95ff4ea1cbab36  f830071 
biology/py-valerius: New port: Python bioinformatics tools
Sun, 7 Aug 2022
[ 20:30 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:d17e67375da9982575cd787209be8775c6f1b491  commit hash:d17e67375da9982575cd787209be8775c6f1b491  commit hash:d17e67375da9982575cd787209be8775c6f1b491  d17e673 
biology/kmcp: New port:  Accurate metagenomic profiling & fast large-scale
genome searching
Thu, 7 Jul 2022
[ 01:33 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:d3e958636916e711fa0437b21b617c16f026d64e  commit hash:d3e958636916e711fa0437b21b617c16f026d64e  commit hash:d3e958636916e711fa0437b21b617c16f026d64e  d3e9586 
biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools

This reverts commit 1cb8897f610a381ddf2802eb09acfba97b15b505.

sra-tools needs to be updated first.

Reported by:	Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@
Wed, 6 Jul 2022
[ 19:03 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:1cb8897f610a381ddf2802eb09acfba97b15b505  commit hash:1cb8897f610a381ddf2802eb09acfba97b15b505  commit hash:1cb8897f610a381ddf2802eb09acfba97b15b505  1cb8897 
biology/ngs-sdk: Remove, ngs was moved into sra-tools
Sun, 19 Jun 2022
[ 07:52 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:db283c306304a61abbea65249f40fb06c1393232  commit hash:db283c306304a61abbea65249f40fb06c1393232  commit hash:db283c306304a61abbea65249f40fb06c1393232  db283c3  (Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
biology/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take
maintainership
Sun, 1 May 2022
[ 17:37 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:8db0b60850a52a1fb0030091485455e07f88912a  commit hash:8db0b60850a52a1fb0030091485455e07f88912a  commit hash:8db0b60850a52a1fb0030091485455e07f88912a  8db0b60 
biology/py-mrcfile: New port: MRC file I/O library which is used in structural
biology
Sat, 19 Mar 2022
[ 12:25 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:a47115b9cad4784d5923f6a6e3d0fbef28623e8f  commit hash:a47115b9cad4784d5923f6a6e3d0fbef28623e8f  commit hash:a47115b9cad4784d5923f6a6e3d0fbef28623e8f  a47115b 
biology/fastq-trim: Lightening fast sequence read trimmer

Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq.
Thu, 3 Feb 2022
[ 19:38 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:d936c94c64a84e88f8c9fbe350aa0445fda80a06  commit hash:d936c94c64a84e88f8c9fbe350aa0445fda80a06  commit hash:d936c94c64a84e88f8c9fbe350aa0445fda80a06  d936c94 
biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)

Read and write Generic Feature Format (GFF) with Biopython integration.

Also adding py-dna-features-viewer to Makefile, missed on last commit
Sun, 5 Dec 2021
[ 20:50 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:864d4fdd1804d2d4f46619f781e397b9ccdf1639  commit hash:864d4fdd1804d2d4f46619f781e397b9ccdf1639  commit hash:864d4fdd1804d2d4f46619f781e397b9ccdf1639  864d4fd 
biology/libgff: GFF/GTF parsing library based on GCLib

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.
Fri, 3 Dec 2021
[ 13:41 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:9152cfc775fca98435610da5faad6d56c5cdeacb  commit hash:9152cfc775fca98435610da5faad6d56c5cdeacb  commit hash:9152cfc775fca98435610da5faad6d56c5cdeacb  9152cfc 
biology/bio-mocha: bcftools plugin for mosaic chromosomal alterations

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.
Wed, 10 Nov 2021
[ 20:49 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:8d2198bb6d6b84739448087c8284079281149086  commit hash:8d2198bb6d6b84739448087c8284079281149086  commit hash:8d2198bb6d6b84739448087c8284079281149086  8d2198b 
biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc

GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.
Mon, 25 Oct 2021
[ 15:57 Po-Chuan Hsieh (sunpoet) search for other commits by this committer ]    commit hash:70b81836d936aa2ade6db83a23f5500b339a4da2  commit hash:70b81836d936aa2ade6db83a23f5500b339a4da2  commit hash:70b81836d936aa2ade6db83a23f5500b339a4da2  70b8183 
*/Makefile: Sort SUBDIRs
Thu, 14 Oct 2021
[ 11:51 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:799d4cc2cfd1c343f486afbde5cc735ec206de2e  commit hash:799d4cc2cfd1c343f486afbde5cc735ec206de2e  commit hash:799d4cc2cfd1c343f486afbde5cc735ec206de2e  799d4cc 
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data

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.
Wed, 13 Oct 2021
[ 21:21 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:ad5a0604c41c81a053224fc6eb949d9390ac0627  commit hash:ad5a0604c41c81a053224fc6eb949d9390ac0627  commit hash:ad5a0604c41c81a053224fc6eb949d9390ac0627  ad5a060 
biology/py-bigwig: Rename to biology/py-pybigwig

Fully match upstream name
[ 18:57 Antoine Brodin (antoine) search for other commits by this committer ]    commit hash:6a226290f3c82253f50151496168e5d1d1bb13c0  commit hash:6a226290f3c82253f50151496168e5d1d1bb13c0  commit hash:6a226290f3c82253f50151496168e5d1d1bb13c0  6a22629 
biology/py-pybigwig: remove, duplicate of biology/py-bigwig
[ 16:02 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:c69e97e63ac3e13459149271dc034ce7b0fdcf35  commit hash:c69e97e63ac3e13459149271dc034ce7b0fdcf35  commit hash:c69e97e63ac3e13459149271dc034ce7b0fdcf35  c69e97e 
biology/py-pybigwig: Fix poudriere build

Typo in post-install
[ 13:03 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:904a889fd144ce50db4d97a702861aea89fe2e94  commit hash:904a889fd144ce50db4d97a702861aea89fe2e94  commit hash:904a889fd144ce50db4d97a702861aea89fe2e94  904a889 
biology/py-pybigwig: Python access to bigWig files using libBigWig

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.
[ 12:53 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:d92344039b4350674d959be16d5a2cfe07f87172  commit hash:d92344039b4350674d959be16d5a2cfe07f87172  commit hash:d92344039b4350674d959be16d5a2cfe07f87172  d923440 
biology/py-py2bit: Python interface for 2bit packed nucleotide files

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.
Tue, 12 Oct 2021
[ 16:40 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2  commit hash:cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2  commit hash:cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2  cdf2ff2 
biology/bamutil: Utilities for working with SAM/BAM files

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.
Fri, 8 Oct 2021
[ 17:20 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:c38052dfd62bdeda93241d0bf88770b8e53a17c5  commit hash:c38052dfd62bdeda93241d0bf88770b8e53a17c5  commit hash:c38052dfd62bdeda93241d0bf88770b8e53a17c5  c38052d 
biology/libneurosim: New port: Common interfaces for neuronal simulators
Tue, 21 Sep 2021
[ 03:35 Po-Chuan Hsieh (sunpoet) search for other commits by this committer ]    commit hash:6e0aa01726fff1d3411c9f1017becf4689d0c465  commit hash:6e0aa01726fff1d3411c9f1017becf4689d0c465  commit hash:6e0aa01726fff1d3411c9f1017becf4689d0c465  6e0aa01 
*/Makefile: Sort SUBDIRs
Sun, 19 Sep 2021
[ 18:15 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:d8c851df599b59e45eea03ee8a16af78602be1f0  commit hash:d8c851df599b59e45eea03ee8a16af78602be1f0  commit hash:d8c851df599b59e45eea03ee8a16af78602be1f0  d8c851d 
biology/py-libsedml: New port: SED-ML library for Python
[ 18:15 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:dd804e98719a5c2376d15b79e6b745f45ab1de40  commit hash:dd804e98719a5c2376d15b79e6b745f45ab1de40  commit hash:dd804e98719a5c2376d15b79e6b745f45ab1de40  dd804e9 
biology/libsedml: New port: C++ SED-ML library
[ 06:47 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:74c998634a3910153179e59ed3fa5f43df3d7332  commit hash:74c998634a3910153179e59ed3fa5f43df3d7332  commit hash:74c998634a3910153179e59ed3fa5f43df3d7332  74c9986 
biology/py-libnuml: New port: Numerical Markup Language for Python
[ 06:47 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:ad2bdb6508797ea89b8e554df96ebbd08b6835ee  commit hash:ad2bdb6508797ea89b8e554df96ebbd08b6835ee  commit hash:ad2bdb6508797ea89b8e554df96ebbd08b6835ee  ad2bdb6 
biology/libnuml: New port: C++ library for Numerical Markup Language
Tue, 7 Sep 2021
[ 20:32 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:e61df5e464758cb1d460c95b4fbb3855a4f7f6dc  commit hash:e61df5e464758cb1d460c95b4fbb3855a4f7f6dc  commit hash:e61df5e464758cb1d460c95b4fbb3855a4f7f6dc  e61df5e 
biology/sam2pairwise: Show pairwise alignment for each read in a SAM file

sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
reconstruct the pairwise alignment of each read.
Mon, 6 Sep 2021
[ 12:55 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:c085af1e81472458f64d957aab5e9a9e0580d8ca  commit hash:c085af1e81472458f64d957aab5e9a9e0580d8ca  commit hash:c085af1e81472458f64d957aab5e9a9e0580d8ca  c085af1 
biology/py-pywgsim: Modified wgsim genomic data simulator

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.
Mon, 30 Aug 2021
[ 13:09 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:904aa60469601239cefbb5dde7f5aa33ccac9a21  commit hash:904aa60469601239cefbb5dde7f5aa33ccac9a21  commit hash:904aa60469601239cefbb5dde7f5aa33ccac9a21  904aa60 
biology/biolibc-tools: High-performance tools based on biolibc

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.
Mon, 23 Aug 2021
[ 17:28 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:2e559ca48c93b075905245367e11e30b9be34b2c  commit hash:2e559ca48c93b075905245367e11e30b9be34b2c  commit hash:2e559ca48c93b075905245367e11e30b9be34b2c  2e559ca 
biology/bfc: Correct sequencing errors from Illumina sequencing data

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.
[ 17:26 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3  commit hash:615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3  commit hash:615c521bb3a0eafdb69e45fc8ddb2ca7c8c286b3  615c521 
biology/flash: Fast Length Adjustment of SHort reads

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.
Tue, 17 Aug 2021
[ 21:30 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:1c0e78eb4b2833ec20fb0addbb001e1e99235982  commit hash:1c0e78eb4b2833ec20fb0addbb001e1e99235982  commit hash:1c0e78eb4b2833ec20fb0addbb001e1e99235982  1c0e78e 
biology/py-PySCeS: New port: Python Simulator for Cellular Systems
[ 21:30 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:10875d93bb728801a61c3d78a1e140718fd0cfdf  commit hash:10875d93bb728801a61c3d78a1e140718fd0cfdf  commit hash:10875d93bb728801a61c3d78a1e140718fd0cfdf  10875d9 
biology/py-python-libsbml: New port: LibSBML Python API
[ 07:05 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:aa9a35be045fdf6852eecb8f78c5c820c9a25611  commit hash:aa9a35be045fdf6852eecb8f78c5c820c9a25611  commit hash:aa9a35be045fdf6852eecb8f78c5c820c9a25611  aa9a35be 
biology/sigviewer: New port: Viewing application for biosignals
[ 02:51 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:df70b7efede8c1936ae5c1867aa0910b99c34ab9  commit hash:df70b7efede8c1936ae5c1867aa0910b99c34ab9  commit hash:df70b7efede8c1936ae5c1867aa0910b99c34ab9  df70b7e 
biology/biosig: New port: Library for reading and writing different biosignal
data format
Fri, 13 Aug 2021
[ 13:34 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:5797d6a3298ebfe3990db73084f34ed935911efa  commit hash:5797d6a3298ebfe3990db73084f34ed935911efa  commit hash:5797d6a3298ebfe3990db73084f34ed935911efa  5797d6a 
biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files

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
Fri, 9 Jul 2021
[ 12:26 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:e44f917e298a1f860fab0790aacd348cae60f74b  commit hash:e44f917e298a1f860fab0790aacd348cae60f74b  commit hash:e44f917e298a1f860fab0790aacd348cae60f74b  e44f917 
biology/erminej: Analyses of gene sets, e.g. gene expression profiling

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).
Fri, 2 Jul 2021
[ 17:00 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:7fd4d4420f371474514cdb696d120e069b11ec21  commit hash:7fd4d4420f371474514cdb696d120e069b11ec21  commit hash:7fd4d4420f371474514cdb696d120e069b11ec21  7fd4d44 
biology/py-goatools: Tools for processing and visualizing Gene Ontology terms

Goatools is a python library for processing Gene Ontology (GO) terms.  It
includes routines for processing, filtering, and visualizing GO data.
Thu, 24 Jun 2021
[ 17:31 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:cf14bbb325bb8696c275ebbabff3da95a75815eb  commit hash:cf14bbb325bb8696c275ebbabff3da95a75815eb  commit hash:cf14bbb325bb8696c275ebbabff3da95a75815eb  cf14bbb 
biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite

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.
Tue, 22 Jun 2021
[ 17:55 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:69656bf0d7d99660e536c22472a5eae639695a97  commit hash:69656bf0d7d99660e536c22472a5eae639695a97  commit hash:69656bf0d7d99660e536c22472a5eae639695a97  69656bf  (Only the first 10 of 45 ports in this commit are shown above. View all ports for this commit)
biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read
Archives

SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.

SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.

This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree.  Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port.  We are working
with upstream with hope for long-term improvements.
Fri, 18 Jun 2021
[ 21:56 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:6df92a09ad7a75d3533ac3510cba668c74689255  commit hash:6df92a09ad7a75d3533ac3510cba668c74689255  commit hash:6df92a09ad7a75d3533ac3510cba668c74689255  6df92a0 
biology/biostar-tools: Meta-port for Biostar Handbook tools

Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions.  If you need bedGraphToBigWig, run

    cd /usr/ports/biology/ucsc-userapps && make install clean
Mon, 14 Jun 2021
[ 16:40 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:5a2a6eb32954aa49c79269b08fd7e26ca4436f3d  commit hash:5a2a6eb32954aa49c79269b08fd7e26ca4436f3d  commit hash:5a2a6eb32954aa49c79269b08fd7e26ca4436f3d  5a2a6eb 
biology/peak-classifier: Classify peaks based on GFF features

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons.  This is the default for
common data sources.
Wed, 26 May 2021
[ 22:25 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:5b018ca96217b47530cb3e48dd6f869be279ebaa  commit hash:5b018ca96217b47530cb3e48dd6f869be279ebaa  commit hash:5b018ca96217b47530cb3e48dd6f869be279ebaa  5b018ca 
biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit
[ 22:25 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:be2fb2f2905d13d5f2463688dbf319f5940cfccc  commit hash:be2fb2f2905d13d5f2463688dbf319f5940cfccc  commit hash:be2fb2f2905d13d5f2463688dbf319f5940cfccc  be2fb2f 
biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set
operations on k-mers
Wed, 12 May 2021
[ 01:21 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:37be6965367eec49bc848623a2ad782d8f74471a  commit hash:37be6965367eec49bc848623a2ad782d8f74471a  commit hash:37be6965367eec49bc848623a2ad782d8f74471a  37be696 
New port: biology/seqan3: C++ header-only library for biological sequence
analysis
Sun, 25 Apr 2021
[ 17:47 Antoine Brodin (antoine) search for other commits by this committer ]    commit hash:28164db7c511fe640cb2adf1dff10362897cf304  commit hash:28164db7c511fe640cb2adf1dff10362897cf304  commit hash:28164db7c511fe640cb2adf1dff10362897cf304  28164db 
Hook biology/ucsc-userapps to the build
Sat, 24 Apr 2021
[ 23:40 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:ab50f8435a78a574ac5ce683004b078c5baf209d  commit hash:ab50f8435a78a574ac5ce683004b078c5baf209d  commit hash:ab50f8435a78a574ac5ce683004b078c5baf209d  ab50f84  (Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
biology/ncbi-entrez-direct: Access to the NCBI's interconnected databases

Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.
Tue, 20 Apr 2021
[ 04:22 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:b9f16eadc90f774bff9030ef7b8511ba1a392464  commit hash:b9f16eadc90f774bff9030ef7b8511ba1a392464  commit hash:b9f16eadc90f774bff9030ef7b8511ba1a392464  b9f16ea 
New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and
Resolwe Bioinformatics
Sun, 18 Apr 2021
[ 18:46 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:5164d38ee538f6791a25b81f28a27126b90444f7  commit hash:5164d38ee538f6791a25b81f28a27126b90444f7  commit hash:5164d38ee538f6791a25b81f28a27126b90444f7  5164d38 
biology/snpeff: Genetic variant annotation and effect prediction toolbox

Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).
[ 16:21 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:15458dfbacb842d71a41dcfdb6be83301ef0b7b6  commit hash:15458dfbacb842d71a41dcfdb6be83301ef0b7b6  commit hash:15458dfbacb842d71a41dcfdb6be83301ef0b7b6  15458df 
biology/bbmap: BBMap short read aligner, and other bioinformatic tools

This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.
[ 13:53 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:49a1ada63293e4c27a396fb8997a238dd090e7de  commit hash:49a1ada63293e4c27a396fb8997a238dd090e7de  commit hash:49a1ada63293e4c27a396fb8997a238dd090e7de  49a1ada 
biology/readseq: Read and reformat biosequences, Java command-line version

Sequence reading library developed by the Ribosomal Database Project.  It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.
Fri, 16 Apr 2021
[ 21:04 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:2aa37d819d48330c1f0e97c95aeb92371ea06690  commit hash:2aa37d819d48330c1f0e97c95aeb92371ea06690  commit hash:2aa37d819d48330c1f0e97c95aeb92371ea06690  2aa37d8 
New port: biology/seqkit: Cross-platform and ultrafast toolkit for FASTA/Q file
manipulation
Mon, 12 Apr 2021
[ 23:37 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:9128727562651ebcc304714cccd03d9643165a74  commit hash:9128727562651ebcc304714cccd03d9643165a74  commit hash:9128727562651ebcc304714cccd03d9643165a74  9128727 
biology/py-crossmap: Lift over genomics coordinates between assemblies

CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.
[ 23:24 Jason W. Bacon (jwb) search for other commits by this committer ]    commit hash:dfcece22a2cb1b45e0cbf8531709250fde686119  commit hash:dfcece22a2cb1b45e0cbf8531709250fde686119  commit hash:dfcece22a2cb1b45e0cbf8531709250fde686119  dfcece2 
biology/py-bigwig: Python access to bigWig files using libBigWig

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.
[ 09:29 Yuri Victorovich (yuri) search for other commits by this committer ]    commit hash:d55fba431adf6bc61c3553dd91625a4b16115cf6  commit hash:d55fba431adf6bc61c3553dd91625a4b16115cf6  commit hash:d55fba431adf6bc61c3553dd91625a4b16115cf6  d55fba4  (Only the first 10 of 31 ports in this commit are shown above. View all ports for this commit)
New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequence
Read Archive

PR:		223273
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (original version)
Wed, 7 Apr 2021
[ 17:54 Rene Ladan (rene) search for other commits by this committer ]    commit hash:5980fd40bc59f3f872f57f75b3a31fb986c1b06e  commit hash:5980fd40bc59f3f872f57f75b3a31fb986c1b06e  commit hash:5980fd40bc59f3f872f57f75b3a31fb986c1b06e  5980fd4  (Only the first 10 of 376 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
(Only the first 15 lines of the commit message are shown above View all of this commit message)
[ 08:09 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  cf118cc  (Only the first 10 of 8873 ports in this commit are shown above. View all ports for this commit)
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
Tue, 6 Apr 2021
[ 14:31 Mathieu Arnold (mat) search for other commits by this committer ]    commit hash:305f148f482daf30dcf728039d03d019f88344eb  commit hash:305f148f482daf30dcf728039d03d019f88344eb  commit hash:305f148f482daf30dcf728039d03d019f88344eb  305f148  (Only the first 10 of 29333 ports in this commit are shown above. View all ports for this commit)
Remove # $FreeBSD$ from Makefiles.
Tue, 23 Mar 2021
[ 16:32 jwb search for other commits by this committer ] Original commit   Revision:569036
biology/vcf2hap: Generate .hap file from VCF for haplohseq

vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq.  vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.
[ 15:15 jwb search for other commits by this committer ] Original commit   Revision:569033
biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file

ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.
Sun, 21 Mar 2021
[ 15:17 jwb search for other commits by this committer ] Original commit   Revision:568922
biology/vcf-split: Split a multi-sample VCF into single-sample VCFs

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously.  Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.
[ 15:10 jwb search for other commits by this committer ] Original commit   Revision:568921
biology/biolibc: Low-level high-performance bioinformatics library

Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data.  Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications.  These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.
Mon, 15 Mar 2021
[ 20:09 jwb search for other commits by this committer ] Original commit   Revision:568501
biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF format

Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for
small academic examples or test inputs of arbitrary size.  Output can be piped
directly to programs or redirected to a file and edited to taste.
Sat, 13 Mar 2021
[ 23:37 yuri search for other commits by this committer ] Original commit   Revision:568296
Move: biology/py-fastTSNE -> math/py-openTSNE

Project was renamed and reimplemented.
Tue, 19 Jan 2021
[ 09:49 yuri search for other commits by this committer ] Original commit   Revision:562039
New port: biology/rampler: Standalone module for sampling genomic sequences
[ 09:41 yuri search for other commits by this committer ] Original commit   Revision:562038
New port: biology/edlib: Fast C++ library for sequence alignment using edit
distance
[ 09:28 yuri search for other commits by this committer ] Original commit   Revision:562036
New port: biology/spoa: C++ implementation of the partial order alignment (POA)
algorithm
[ 09:01 yuri search for other commits by this committer ] Original commit   Revision:562035
New port: biology/biosoup: Collection of C++ header-only data structures for
bioinformatics
[ 07:56 yuri search for other commits by this committer ] Original commit   Revision:562033
New port: biology/bioparser: C++ header only parsing library for several formats
in bioinformatics
Thu, 14 Jan 2021
[ 21:44 antoine search for other commits by this committer ] Original commit   Revision:561604
Hook haplohseq to the build
Sun, 15 Nov 2020
[ 18:50 jwb search for other commits by this committer ] Original commit   Revision:555418
biology/pooler: Optimise DNA sequencing primer-set combinations

Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.

Primer Pooler can:

* Check through each proposed pool for combinations that are likely to form
  dimers

* Automatically move prospective amplicons between proposed pools to reduce
  dimer formation

* Automatically search the genome sequence to find which amplicons overlap, and
  place their corresponding primers in separate pools
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Thu, 24 Sep 2020
[ 19:31 jrm search for other commits by this committer ] Original commit   Revision:549943
biology/py-biom-format: Restore in preparation for an update to v2.1.8

Version 2.1.8 supports python 3
Sat, 19 Sep 2020
[ 13:01 rene search for other commits by this committer ] Original commit   Revision:548980 (Only the first 10 of 199 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

2020-09-15 audio/abraca: Uses deprecated version of python
2020-09-15 audio/ardour5: Uses deprecated version of python
2020-09-15 audio/cplay: Uses deprecated version of python
2020-09-15 audio/cpp-xmms2: Uses deprecated version of python
2020-09-15 audio/p5-xmms2: Uses deprecated version of python
2020-09-15 biology/haplohseq: Uses deprecated version of python
2020-09-15 biology/tophat: Uses deprecated version of python
2020-09-15 chinese/ibus-array: Uses deprecated version of python
2020-09-15 comms/congruity: Uses deprecated version of python
2020-09-15 comms/libbtbb: Uses deprecated version of python
2020-09-15 comms/quisk: Uses deprecated version of python
2020-09-15 databases/mtools-mongodb: Uses deprecated version of python
2020-09-15 databases/mydbf2mysql: Uses deprecated version of python
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Thu, 27 Aug 2020
[ 11:25 rene search for other commits by this committer ] Original commit   Revision:546333 (Only the first 10 of 44 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

2020-08-26 audio/timidity++-tcltk: Broken for more than 6 months
2020-08-26 biology/pbcopper: Broken for more than 6 months
2020-08-26 devel/ace: Broken for more than 6 months
2020-08-26 devel/bin86: Broken for more than 6 months
2020-08-26 devel/erlang-oserl: Broken for more than 6 months
2020-08-20 emulators/qemu40: Please consider using qemu or qemu41
2020-08-26 games/linux-darwinia-demo: Broken for more than 6 months
2020-08-26 games/linux-defcon: Broken for more than 6 months
2020-08-26 games/linux-uplink-demo: Broken for more than 6 months
2020-08-26 games/xevil: Broken for more than 6 months
2020-08-26 games/xminesweep: Broken for more than 6 months
2020-08-26 graphics/backfract: Broken for more than 6 months
2020-08-26 japanese/kanjipad: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sat, 15 Aug 2020
[ 10:50 rene search for other commits by this committer ] Original commit   Revision:544927 (Only the first 10 of 219 ports in this commit are shown above. View all ports for this commit)
Remove deprecated ports:

2020-08-15 archivers/py-backports.lzma: Uses deprecated version of python
2020-08-15 archivers/py-bup: Uses deprecated version of python
2020-08-15 archivers/py-librtfcomp: Uses deprecated version of python
2020-08-15 audio/blop-lv2: Uses deprecated version of python
2020-08-15 audio/bs2b-lv2: Uses deprecated version of python
2020-08-15 audio/py-gmusicproxy: Uses deprecated version of python
2020-08-15 audio/py-karaoke: Uses deprecated version of python
2020-08-15 audio/py-openal: Uses deprecated version of python
2020-08-15 audio/py-py-jack: Uses deprecated version of python
2020-08-15 audio/py-xmms2: Uses deprecated version of python
2020-08-15 audio/triceratops-lv2: Uses deprecated version of python
2020-08-15 biology/py-biom-format: Uses deprecated version of python
2020-08-15 comms/py-bulksms: Uses deprecated version of python
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Fri, 24 Jul 2020
[ 07:08 sunpoet search for other commits by this committer ] Original commit   Revision:543012
Add rubygem-bio-shell 1.0.0

bio-shell, providing BioRuby Shell, is a command-line interface for BioRuby, an
open source bioinformatics library for Ruby.

This code has historically been part of the BioRuby gem, but has been split into
its own gem as part of an effort to modularize BioRuby. bio-shell and many more
plugins are available at biogems.info.

WWW: https://github.com/bioruby/bioruby-shell
[ 07:08 sunpoet search for other commits by this committer ] Original commit   Revision:543011
Add rubygem-bio-old-biofetch-emulator 1.0.0

bio-old-biofetch-emulator emulates Bio::Fetch object in BioRuby as if
discontinued BioRuby BioFetch server were still alive. It overrides methods and
objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it
intercepts all requests and converts them into existing web services such as
TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp).

WWW: https://github.com/ngoto/bioruby-old-biofetch-emulator
[ 07:08 sunpoet search for other commits by this committer ] Original commit   Revision:543010
Add rubygem-bio-executables 1.0.0

bio-executables is a collection of miscellaneous utilities for bioinformatics
that were formerly part of the BioRuby core ("bio" gem). Because of reducing
complexity, they were moved to this gem.

This code has historically been part of the BioRuby gem, but has been split into
its own gem as part of an effort to modularize BioRuby. bio-executables and many
more plugins are available at biogems.info.

WWW: https://github.com/bioruby/bioruby-executables
Sat, 13 Jun 2020
[ 13:54 jwb search for other commits by this committer ] Original commit   Revision:538672
biology/picard-tools: CLI tools for manipulating sequencing data

Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
Fri, 5 Jun 2020
[ 02:45 jwb search for other commits by this committer ] Original commit   Revision:537983
biology/bioawk: BWK awk modified for biological data

Bioawk is an extension to Brian Kernighan's awk, adding the support of several
common biological data formats, including optionally gzip'ed BED, GFF, SAM,
VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
built-in functions and an command line option to use TAB as the input/output
delimiter. When the new functionality is not used, bioawk is intended to behave
exactly the same as the original BWK awk.
[ 01:55 jwb search for other commits by this committer ] Original commit   Revision:537982 (Only the first 10 of 20 ports in this commit are shown above. View all ports for this commit)
biology/subread: Read alignment, quantification and mutation discovery

The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.
Thu, 4 Jun 2020
[ 18:28 jwb search for other commits by this committer ] Original commit   Revision:537926 (Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
bioloty/vt: Discovers short variants from Next Generation Sequencing data
Sat, 16 May 2020
[ 03:11 yuri search for other commits by this committer ] Original commit   Revision:535347
New port: biology/py-hits: Utilities for processing high-throughput sequencing
experiments
[ 02:25 yuri search for other commits by this committer ] Original commit   Revision:535344
New port: biology/py-scikit-bio: Data structures, algorithms, educational
resources for bioinformatics
[ 00:14 yuri search for other commits by this committer ] Original commit   Revision:535340
New port: biology/py-pandas-charm: Library for getting character matrices into
and out of pandas
[ 00:13 yuri search for other commits by this committer ] Original commit   Revision:535339
New port: biology/py-ete3: Framework for the analysis and visualization of trees
Fri, 15 May 2020
[ 04:58 yuri search for other commits by this committer ] Original commit   Revision:535266
New port: biology/scrm: Coalescent simulator for biological sequences
Sun, 10 May 2020
[ 15:42 danfe search for other commits by this committer ] Original commit   Revision:534852
- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead
Tue, 5 May 2020
[ 15:38 rene search for other commits by this committer ] Original commit   Revision:534093 (Only the first 10 of 492 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)

Number of commits found: 309 (showing only 100 on this page)

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