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2022-12-12biology/Makefile: Add rna-seq meta-packagebacon1-1/+2
2022-12-12biology/Makefile: Add fasdabacon1-1/+2
2022-11-28Add balance-tuipin1-1/+2
2022-11-06biology/Makefile: Add gffreadbacon1-1/+2
2022-11-06biology/Makefile: Add fastq-trimbacon1-1/+2
2022-04-05biology/Makefile: Add fastx-toolkitbacon1-1/+2
2022-02-17py-mol: removewiz1-2/+1
This package is from 2012, the current version is from 2020. A replacement candidate is in wip/py-mol but needs more work. One of the last users of py-numpy16 in pkgsrc.
2021-08-31biology/Makefile: Add biolibc-toolsbacon1-1/+2
2021-06-15biology/Makefile: Add peak-classifierbacon1-1/+2
2021-05-27biology/filter-fastq: add filter-fastq version 0.0.0.20210527brook1-1/+2
2021-05-26Added biology/beagle version 5.2brook1-1/+2
2021-05-26Added biology/racon 1.4.3brook1-1/+2
2021-05-26Add biology/minimap2 2.18brook1-1/+2
2021-05-26Add biology/miniasm 0.3.brook1-1/+2
2021-03-24biology/Makefile: Add vcf2hapbacon1-1/+2
2021-03-24biology/Makefile: Add ad2vcfbacon1-1/+2
2021-03-24biology/Makefile: Add biolibc, vcf-splitbacon1-1/+3
2021-03-21biology/Makefile: Add generandbacon1-1/+2
2021-02-24biology/Makefile: + igvwiz1-1/+2
2021-02-12biology/Makefile: sort entriesgutteridge1-3/+3
2021-02-08biology/Makefile: Add py-cutadaptbacon1-1/+2
2021-02-08biology/Makefile: Add py-dnaiobacon1-1/+2
2021-01-22biology/Makefile: Add bedtoolsbacon1-1/+2
2021-01-21biology/Makefile: Add bowtie2bacon1-1/+2
2021-01-20biology/Makefile: Add fastqcbacon1-1/+2
2020-12-18Add biology/molsketchpin1-1/+2
2020-11-03New package, coordgenlibs-1.4.2.bsiegert1-1/+2
Part of PR pkg/55755. This is Schroedinger, Inc's 2D coordinate generation. It was formerly proprietary code, but is now released under the BSD license. The emphasis of these algorithms are on quality of 2D coordinates rather than speed of generation. The algorithm distinguishes itself from many others by doing well with both macrocycles and metal complexes. It also does extremely well on typical drug-like small molecules, and has been validated on millions of compounds.
2020-11-03New package, maeparser-1.4.2.bsiegert1-1/+2
maeparser is a parser for Schrodinger Maestro files. Structure files (.mae,.maegz,.mae.gz) can contain multiple structures delimited by "f_m_ct". See MaeConstants.hpp for standard block and property names.
2020-08-10biology/R-popbio: import R-popbio-2.7brook1-1/+2
Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
2019-08-09py-biopython: initial commitbrook1-1/+2
The Biopython package contains high-quality, reusable modules and scripts written in Python to make it as easy as possible to use Python for bioinformatics. The Biopython includes the follwing: the ability to parse bioinformatics files into python utilizable data structures, including support for the formats such as Blast output, Clustalw, FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP, Rebase, UniGene, and SwissProt.
2019-05-10Add vsearchbacon1-1/+2
2019-05-04Add fastpbacon1-1/+2
2019-01-15Add hisat2bacon1-1/+2
2019-01-07Add canubacon1-1/+2
2018-12-22Add stacksbacon1-1/+2
2018-12-21Add kallistobacon1-1/+2
2018-11-15bcftools: added version 1.9adam1-1/+2
BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. In order to avoid tedious repetion, throughout this document we will use "VCF" and "BCF" interchangeably, unless specifically noted. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF work in all situations. Unindexed VCF and BCF and streams work in most, but not all situations. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed.
2018-10-31biology: +py-pydicomleot1-1/+2
2018-07-25Add trimmomaticbacon1-1/+2
2018-05-07Add samtoolsbacon1-1/+2
2018-04-30Add htslibbacon1-1/+2
2018-04-27Add ncbi-blast+bacon1-1/+2
2017-05-10 Deleting p5-BioPerl. Duplicate with bioperl. Sorry.mef1-2/+1
2017-05-07Added biology/p5-BioPerl version 1.007001mef1-1/+2
2015-10-14Add bwa.leot1-1/+2
2015-10-12Add cdhit.leot1-1/+2
2015-07-22+ gabeditasau1-1/+2
2014-02-20Add p5-Bio-ASN1-EntrezGenefhajny1-1/+2
2013-03-16+ mpqcasau1-1/+2
2012-11-01+ plinkseqasau1-1/+2
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-25 20:44:08 +0000