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https://www.aquamaniac.de/rdm/projects/libchipcard
Software library for generic access to chipcard readers and cards
Proper citation: Libchipcard (RRID:SCR_024071) Copy
https://sw-tools.rcsb.org/apps/CORE-WRAPPER/index.html
Software library that exports C++ mmCIF accessors to Python.
Proper citation: Core Wrapper (RRID:SCR_024087) Copy
https://github.com/mtholder/ncl
Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored.
Proper citation: libncl (RRID:SCR_024080) Copy
https://github.com/kdm9/libqes
Software C library with bioinformatic focus optimised for speed and clean API.
Proper citation: libqes (RRID:SCR_024083) Copy
https://sourceforge.net/projects/tab2mage/
Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
Proper citation: Tab2MAGE (RRID:SCR_024101) Copy
http://colibread.inria.fr/software/mapsembler2/
Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants.
Proper citation: Mapsembler2 (RRID:SCR_024102) Copy
https://github.com/gerddie/maxflow
Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph.
Proper citation: MAXFLOW (RRID:SCR_024103) Copy
https://neobio.sourceforge.net/
Software library of sequence alignment algorithms implemented in Java.
Proper citation: NeoBio (RRID:SCR_024131) Copy
http://murasaki.dna.bio.keio.ac.jp/wiki/
Software language-theory based homology detection tool across multiple large genomes.
Proper citation: Murasaki (RRID:SCR_024132) Copy
https://www.ncbi.nlm.nih.gov/books/NBK179288/
Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats.
Proper citation: Entrez Direct (RRID:SCR_024136) Copy
https://doua.prabi.fr/software/njplot
Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.
Proper citation: NJplot (RRID:SCR_024137) Copy
https://github.com/mroosmalen/nanosv
Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
Proper citation: NanoSV (RRID:SCR_024127) Copy
https://github.com/WorkflowConversion/CTDConverter
Software Python scripts to convert CTD files into other formats such as Galaxy, CWL.
Proper citation: CTDConverter (RRID:SCR_024007) Copy
https://github.com/wdecoster/NanoPlot
Software package as plotting tool for long read sequencing data and alignments.
Proper citation: NanoPlot (RRID:SCR_024128) Copy
https://pypi.org/project/OBITools/
Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses.
Proper citation: OBITools (RRID:SCR_024141) Copy
https://freeimage.sourceforge.io/
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Proper citation: FreeImage (RRID:SCR_024022) Copy
https://www.orthanc-server.com/
Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases.
Proper citation: Orthanc (RRID:SCR_024145) Copy
https://www.rostlab.org/owiki/index.php/Norsnet
Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.
Proper citation: NORSnet (RRID:SCR_024146) Copy
https://github.com/bioinfo-ut/GenomeTester4
Software toolkit for performing set operations - union, intersection and complement on k-mer lists.
Proper citation: GenomeTester4 (RRID:SCR_024026) Copy
Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers.
Proper citation: OpenSurgSim (RRID:SCR_024147) Copy
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