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https://github.com/husonlab/jloda

Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN.

Proper citation: JLODA (RRID:SCR_024076) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.com/german.tischler/libmaus2

Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes.

Proper citation: libmaus2 (RRID:SCR_024077) Copy   

•   Source: SciCrunch Registry
  

https://www.aquamaniac.de/rdm/projects/libchipcard

Software library for generic access to chipcard readers and cards

Proper citation: Libchipcard (RRID:SCR_024071) Copy   

•   Source: SciCrunch Registry
  

http://liorkirsch.github.io/brain-heatmap-web/

Custom Brain Heatmaps on top of the Allen Brain Atlas. Platform to generate brain heatmaps for the human or mouse brain ontop of the Allen Brain Atlas by editing google spreadsheet template with specific brain region and gene information.

Proper citation: Brain heatmap (RRID:SCR_023815) Copy   

•   Source: SciCrunch Registry
  

https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX.

Proper citation: Cell Ranger ARC (RRID:SCR_023897) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vcflib/tabixpp

Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer

Proper citation: tabixpp (RRID:SCR_024107) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/brentp/cyvcf2

Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis.

Proper citation: cyvcf2 (RRID:SCR_024000) Copy   

•   Source: SciCrunch Registry
  

http://www.commontk.org/

Software to support biomedical image computing.

Proper citation: CTK (RRID:SCR_024002) Copy   

•   Source: SciCrunch Registry
  

https://github.com/wdecoster/nanolyse

Software package to remove reads mapping to the lambda phage genome from a fastq file.

Proper citation: NanoLyse (RRID:SCR_024125) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

https://github.com/kdm9/libqes

Software C library with bioinformatic focus optimised for speed and clean API.

Proper citation: libqes (RRID:SCR_024083) Copy   

•   Source: SciCrunch Registry
  

https://neurobridges.org/

Platform for data discovery to enhance the reuse of clinical neuroscience and neuroimaging data. Provides NeuroBridge ontology, and combines machine learning with ontology based search of both neuroimaging repositories like XNAT databases and open access full text journals such as PubMed Central. Connects researchers with potential neuroimaging data, by searching text of papers describing neuroimaging studies that contain information on neuroimaging data.

Proper citation: NeuroBridge (RRID:SCR_023703) Copy   

•   Source: SciCrunch Registry
  

https://www.cia.gov/the-world-factbook/about/

Presents basic realities about world in which we live in and is one of the U.S. Government’s most accessed publications. Provides basic intelligence on history, people, government, economy, energy, geography, environment, communications, transportation, military, terrorism, and transnational issues for 266 world entities.

Proper citation: The World Factbook (RRID:SCR_023548) Copy   

•   Source: SciCrunch Registry
  

http://fair.dei.unipd.it/software/

Software platform for integration of imaging data and Allen Human Brain Atlas mRNA data. MENGA investigates correlation patterns between various imaging modalities and gene expression profiles based on the Allen Brain Atlas in order to create comprehensive, integrated data platform.

Proper citation: Multimodal Environment for Neuroimaging and Genomic Analysis (RRID:SCR_023822) Copy   

•   Source: SciCrunch Registry
  

https://github.com/toddy15/medicalterms

Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words.

Proper citation: medicalterms (RRID:SCR_024117) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/oculomatic-eye-tracking/

Project related to investigate mechanisms of oculomotor behavior.Included system is provided by New York University scientists to track eye movement.System includes camera module, lens, IR-Light source, mounting solution, data acquisition device, and general purpose PC. System consists of open source software and modular hardware solution to eye tracking for use in humans and non-human primates.

Proper citation: Oculomatic Eye Tracking project (RRID:SCR_021465) Copy   

•   Source: SciCrunch Registry
  

https://github.com/scimemia/M-Track

Software toolbox for automated detection of forepaw trajectories in mice.Open source code to simultaneously track movement of individual paws during spontaneous grooming episodes and walking in multiple freely behaving mice/rats.

Proper citation: M-Track (RRID:SCR_021508) Copy   

•   Source: SciCrunch Registry
  

http://nf.synapse.org

Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases.

Proper citation: NF Data Portal (RRID:SCR_021683) Copy   

•   Source: SciCrunch Registry
  

https://edspace.american.edu/openbehavior/project/moving-wall-box-mwb/

Portal provides Moving Wall Box system used to testing strategy task where mouse is repeatedly forced to jump over small ice by slowly moving walls whereby presence of animal is automatically sensed via balances and analyzed by microcontroller board which in turn controls movements of walls. Device provided by Max Planck Institute of Psychiatry scientist. Used for repeated assessment of fear coping strategies.

Proper citation: Moving Wall Box (RRID:SCR_021559) Copy   

•   Source: SciCrunch Registry