Difference between revisions of "Biology"
From GhostBSD Wiki
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|[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl-Run/pkg-descr?revision=HEAD]] [[https://github.com/bioperl/bioperl-run]] | |[[https://svnweb.freebsd.org/ports/head/biology/p5-BioPerl-Run/pkg-descr?revision=HEAD]] [[https://github.com/bioperl/bioperl-run]] | ||
|- | |- | ||
| − | | | + | |p5-TrimGalore |
| − | |[[]] [[]] | + | |Wrapper around Cutadapt and FastQC for adapter and quality trimming |
| + | |[[https://svnweb.freebsd.org/ports/head/biology/p5-TrimGalore/pkg-descr?revision=HEAD]] [[https://github.com/FelixKrueger/TrimGalore]] | ||
|- | |- | ||
| − | | | + | |pbcopper |
| − | |[[]] [[]] | + | |Core C++ library for Pacific Biosciences tools |
| + | |[[https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[https://github.com/PacificBiosciences/pbcopper]] | ||
|- | |- | ||
| − | | | + | |prodigal |
| − | |[[]] [[]] | + | |Protein-coding gene prediction for prokaryotic genomes |
| + | |[[https://svnweb.freebsd.org/ports/head/biology/prodigal/pkg-descr?revision=HEAD]] [[https://github.com/hyattpd/Prodigal]] | ||
|- | |- | ||
| − | | | + | |py27-multiqc |
| − | |[[]] [[]] | + | |Aggregate bioinformatics analysis reports across samples and tools |
| + | |[[https://svnweb.freebsd.org/ports/head/biology/py-multiqc/pkg-descr?revision=HEAD]] [[https://pypi.python.org/pypi/multiqc]] | ||
|- | |- | ||
| − | | | + | |py27-pymol |
| − | |[[]] [[]] | + | |OpenGL-based molecular visualization system |
| + | |[[https://svnweb.freebsd.org/ports/head/science/py-pymol/pkg-descr?revision=HEAD]] [[https://pymol.org/2/]] | ||
|- | |- | ||
| − | | | + | |py37-chainer-chemistry |
| − | |[[]] [[]] | + | |Library for deep learning in biology and chemistry |
| + | |[[https://svnweb.freebsd.org/ports/head/science/py-chainer-chemistry/pkg-descr?revision=HEAD]] [[https://github.com/pfnet-research/chainer-chemistry]] | ||
|- | |- | ||
| | | | ||
Revision as of 05:12, 15 January 2020
Welcome to the Biology
|
| App/Package | Abstract | Addition or Link |
|---|---|---|
| CheckM | Quality assessment tool for the microbial genomes | [[1]] [[2]] |
| GroopM | Metagenomic binning suite | [[3]] [[4]] |
| InsightToolkit | Insight Toolkit | [[5]] [[6]] |
| Jellyfish | Fast, memory-efficient counting of k-mers in DNA | [[7]] [[8]] |
| abyss | Assembly By Short Sequences: parallel, paired-end sequence assembler | [[9]] [[10]] |
| afni | Advanced Functional Neuro Imaging | [[11]] [[12]] |
| artemis | DNA sequence viewer and annotation tool | [[13]] [[14]] |
| avida | Auto-adaptive genetic system designed for ALife research | [[15]] [[16]] |
| babel | Converts among various molecular file formats | [[17]] [[18]] |
| bamtools | API and toolkit for handling BAM files | [[19]] |
| biococoa | Bioinformatics framework | [[20]] [[21]] |
| canu | Single molecule sequence assembler | [[22]] [[23]] |
| cycle | Calendar program for women | [[24]] [[25]] |
| cytoscape | Software to visualize molecular interaction networks, gene expression | [[26]] [[27]] |
| dDocent | Bash pipeline for RAD sequencing | [[28]] [[29]] |
| emboss | Collection of open source tools for genetic sequence analysis | [[30]] [[31]] |
| figtree | Graphical viewer of phylogenetic trees | [[32]] [[33]] |
| garlic | Molecular viewer, editor, and visualization program | [[34]] [[35]] |
| gperiodic | Displays a periodic table of the elements | [[36]] [[37]] |
| haplohseq | Identify regions of allelic imbalance | [[38]] [[39]] |
| hhsuite | Remote protein homology detection suite | [[40]] [[41]] |
| igv | Visualization tool for genomic datasets | [[42]] [[43]] |
| jalview | Viewer and editor for multiple sequence alignments | [[44]] [[45]] |
| kallisto | Quantify abundances of transcripts from RNA-Seq data | [[46]] [[47]] |
| mafft | Multiple alignment program for amino acid or nucleotide sequences | [[48]] [[49]] |
| minc2 | Medical Imaging NetCDF | [[50]] [[51]] |
| molden | Display molecular orbitals and electron densities in 2D and 3D | [[52]] [[53]] |
| ncbi-blast | NCBI implementation of Basic Local Alignment Search Tool | [[54]] [[55]] |
| ncbi-cxx-toolkit- | NCBI C++ Toolkit | [[56]] [[57]] |
| p5-Bio-ASN1-EntrezGene | Regular expression-based Perl Parser for NCBI Entrez Gene | [[58]] [[59]] |
| p5-Bio-Cluster | BioPerl cluster modules | [[60]] [[61]] |
| p5-Bio-Coordinate | Modules for working with biological coordinates | ttps://svnweb.freebsd.org/ports/head/biology/p5-Bio-Coordinate/pkg-descr?revision=HEAD [[62]] |
| p5-Bio-DB-EMBL | Database object interface for EMBL entry retrieval | [[63]] [[64]] |
| p5-Bio-DB-NCBIHelper | Collection of routines useful for queries to NCBI databases | [[65]] [[66]] |
| p5-Bio-Das | Client-side library for Distributed Genome Annotation System | [[67]] [[68]] |
| p5-Bio-Das-Lite | Perl extension for the DAS (HTTP+XML) Protocol | [[69]] [[70]] |
| p5-Bio-FeatureIO | Handler for FeatureIO | [[71]] [[72]] |
| p5-Bio-GFF3 | Fast low-level functions for parsing and formatting GFF3 | [[73]] [[74]] |
| p5-Bio-Glite | Perl Interface to G-language | [[75]] [[76]] |
| p5-Bio-Graphics | Generate GD Images of Bio::Seq Objects | [[77]] [[78]] |
| p5-Bio-MAGETAB | Data model and utility API for the MAGE-TAB format | [[79]] [[80]] |
| p5-Bio-NEXUS | Object-oriented Perl API for the NEXUS file format | [[81]] [[82]] |
| p5-Bio-Phylo | Phylogenetic analysis using Perl | [[83]] [[84]] |
| p5-Bio-SCF | Read and Update SCF Chromatographic Sequence Files | [[85]] [[86]] |
| p5-Bio-Variation | BioPerl variation-related functionality | [[87]] |
| p5-BioPerl | Collection of Perl modules for bioinformatics | [[88]] [[89]] |
| p5-BioPerl-Run | Wrapper modules for common bioinformatics tools | [[90]] [[91]] |
| p5-TrimGalore | Wrapper around Cutadapt and FastQC for adapter and quality trimming | [[92]] [[93]] |
| pbcopper | Core C++ library for Pacific Biosciences tools | [[94]] [[95]] |
| prodigal | Protein-coding gene prediction for prokaryotic genomes | [[96]] [[97]] |
| py27-multiqc | Aggregate bioinformatics analysis reports across samples and tools | [[98]] [[99]] |
| py27-pymol | OpenGL-based molecular visualization system | [[100]] [[101]] |
| py37-chainer-chemistry | Library for deep learning in biology and chemistry | [[102]] [[103]] |
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