Difference between revisions of "Biology"
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|Quantify abundances of transcripts from RNA-Seq data | |Quantify abundances of transcripts from RNA-Seq data | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/kallisto/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pachterlab.github.io/kallisto/about.html]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/kallisto/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://pachterlab.github.io/kallisto/about.html]] | ||
| + | |- | ||
| + | |libghemical | ||
| + | |Support libraries of science/ghemical port | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/libghemical/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.bioinformatics.org/ghemical/ghemical/index.html]] | ||
|- | |- | ||
|mafft | |mafft | ||
|Multiple alignment program for amino acid or nucleotide sequences | |Multiple alignment program for amino acid or nucleotide sequences | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/mafft/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://mafft.cbrc.jp/alignment/software/]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/mafft/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://mafft.cbrc.jp/alignment/software/]] | ||
| + | |- | ||
| + | |massxpert | ||
| + | |massXpert software for (bio)chemists | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/massxpert/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://salsa.debian.org/debichem-team/massxpert]] | ||
|- | |- | ||
|minc2 | |minc2 | ||
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|Display molecular orbitals and electron densities in 2D and 3D | |Display molecular orbitals and electron densities in 2D and 3D | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/molden/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.cmbi.ru.nl/molden/]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/molden/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://www.cmbi.ru.nl/molden/]] | ||
| + | |- | ||
| + | |mmtf-cpp | ||
| + | |C++ MMTF format API, decoder and encoder, for molecular structures | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/mmtf-cpp/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://mmtf.rcsb.org/]] | ||
|- | |- | ||
|ncbi-blast | |ncbi-blast | ||
|NCBI implementation of Basic Local Alignment Search Tool | |NCBI implementation of Basic Local Alignment Search Tool | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://blast.ncbi.nlm.nih.gov]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/ncbi-blast+/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://blast.ncbi.nlm.nih.gov]] | ||
| + | |- | ||
| + | |namd | ||
| + | |Computer software for molecular dynamics simulation | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/science/namd/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://www.ks.uiuc.edu/Research/namd/]] | ||
|- | |- | ||
|ncbi-cxx-toolkit- | |ncbi-cxx-toolkit- | ||
| Line 205: | Line 221: | ||
|Core C++ library for Pacific Biosciences tools | |Core C++ library for Pacific Biosciences tools | ||
|[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/PacificBiosciences/pbcopper]] | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/pbcopper/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=https://github.com/PacificBiosciences/pbcopper]] | ||
| + | |- | ||
| + | |plinkseq | ||
| + | |Toolset for working with human genetic variation data | ||
| + | |[[File:Icon FreeBSD.png|100px|link=https://svnweb.freebsd.org/ports/head/biology/plinkseq/pkg-descr?revision=HEAD]] [[File:1329059652.png|35px|link=http://atgu.mgh.harvard.edu/plinkseq/]] | ||
|- | |- | ||
|prodigal | |prodigal | ||
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!colspan="3"| | !colspan="3"| | ||
|- | |- | ||
| − | !colspan="3"|'''Back to | + | !colspan="3"|'''Back to ''' [[image:Icon Disti GhostBSD.png|50px|link=Science and Engineering]] '''Science and Engineering''' |
| − | + | ||
|} | |} | ||
[[Category:Station]] | [[Category:Station]] | ||
Latest revision as of 13:19, 20 January 2020
Welcome to the Biology
|
| App/Package | Abstract | Addition or Link |
|---|---|---|
| CheckM | Quality assessment tool for the microbial genomes |  
|
| GroopM | Metagenomic binning suite |
|
| InsightToolkit | Insight Toolkit |
|
| Jellyfish | Fast, memory-efficient counting of k-mers in DNA |
|
| abyss | Assembly By Short Sequences: parallel, paired-end sequence assembler |
|
| afni | Advanced Functional Neuro Imaging |
|
| artemis | DNA sequence viewer and annotation tool |
|
| avida | Auto-adaptive genetic system designed for ALife research |
|
| babel | Converts among various molecular file formats |
|
| bamtools | API and toolkit for handling BAM files |
|
| biococoa | Bioinformatics framework |
|
| canu | Single molecule sequence assembler |
|
| cycle | Calendar program for women |
|
| cytoscape | Software to visualize molecular interaction networks, gene expression |
|
| dDocent | Bash pipeline for RAD sequencing |
|
| emboss | Collection of open source tools for genetic sequence analysis |
|
| figtree | Graphical viewer of phylogenetic trees |
|
| garlic | Molecular viewer, editor, and visualization program |
|
| gperiodic | Displays a periodic table of the elements |
|
| haplohseq | Identify regions of allelic imbalance |
|
| hhsuite | Remote protein homology detection suite |
|
| igv | Visualization tool for genomic datasets |
|
| jalview | Viewer and editor for multiple sequence alignments |
|
| kallisto | Quantify abundances of transcripts from RNA-Seq data |
|
| libghemical | Support libraries of science/ghemical port |
|
| mafft | Multiple alignment program for amino acid or nucleotide sequences |
|
| massxpert | massXpert software for (bio)chemists |
|
| minc2 | Medical Imaging NetCDF |
|
| molden | Display molecular orbitals and electron densities in 2D and 3D |
|
| mmtf-cpp | C++ MMTF format API, decoder and encoder, for molecular structures |
|
| ncbi-blast | NCBI implementation of Basic Local Alignment Search Tool |
|
| namd | Computer software for molecular dynamics simulation |
|
| ncbi-cxx-toolkit- | NCBI C++ Toolkit |
|
| p5-Bio-ASN1-EntrezGene | Regular expression-based Perl Parser for NCBI Entrez Gene |
|
| p5-Bio-Cluster | BioPerl cluster modules |
|
| p5-Bio-Coordinate | Modules for working with biological coordinates |
|
| p5-Bio-DB-EMBL | Database object interface for EMBL entry retrieval |
|
| p5-Bio-DB-NCBIHelper | Collection of routines useful for queries to NCBI databases |
|
| p5-Bio-Das | Client-side library for Distributed Genome Annotation System |
|
| p5-Bio-Das-Lite | Perl extension for the DAS (HTTP+XML) Protocol |
|
| p5-Bio-FeatureIO | Handler for FeatureIO |
|
| p5-Bio-GFF3 | Fast low-level functions for parsing and formatting GFF3 |
|
| p5-Bio-Glite | Perl Interface to G-language |
|
| p5-Bio-Graphics | Generate GD Images of Bio::Seq Objects |
|
| p5-Bio-MAGETAB | Data model and utility API for the MAGE-TAB format |
|
| p5-Bio-NEXUS | Object-oriented Perl API for the NEXUS file format |
|
| p5-Bio-Phylo | Phylogenetic analysis using Perl |
|
| p5-Bio-SCF | Read and Update SCF Chromatographic Sequence Files |
|
| p5-Bio-Variation | BioPerl variation-related functionality |
|
| p5-BioPerl | Collection of Perl modules for bioinformatics |
|
| p5-BioPerl-Run | Wrapper modules for common bioinformatics tools |
|
| p5-TrimGalore | Wrapper around Cutadapt and FastQC for adapter and quality trimming |
|
| pbcopper | Core C++ library for Pacific Biosciences tools |
|
| plinkseq | Toolset for working with human genetic variation data |
|
| prodigal | Protein-coding gene prediction for prokaryotic genomes |
|
| py27-multiqc | Aggregate bioinformatics analysis reports across samples and tools |
|
| py27-pymol | OpenGL-based molecular visualization system |
|
| py37-chainer-chemistry | Library for deep learning in biology and chemistry |
|
| py37-multiqc | Aggregate bioinformatics analysis reports across samples and tools |
|
| py37-orange3-bioinformatics | Orange add-on providing common functionality for bioinformatics |
|
| py37-orange3-single-cell | Orange add-on for gene expression of single cell data |
|
| pycogent | Toolkit for statistical analysis of biological sequences |
|
| raster3d | Set of tools for generating raster images of proteins and molecules |
|
| seqtools | Tools for visualising sequence alignments |
|
| ugene | Free, open-source, cross-platform bioinformatics toolkit |
|
| If you don't find a package, you are looking for, we recommend to search the  Ports Collection. If it is there, than it is also in the GhostBSD ports.
| ||
Back to  Science and Engineering
| ||
