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https://bruskolab.diabetes.ufl.edu/research/handel-i/

HANDEL-1 program to better understand normal human immune development by acquiring stromal and mucosal tissues from infant and pediatric organ donors and to create novel and essential dataset informing immune system development in collaborative research project that leverages shared access to various tissues in conjunction with existing HANDEL-P program that seeks to understand development of pancreas and islet microenvironment in early life.

Proper citation: Human Atlas of Neonatal Development and Early Life Immunity (RRID:SCR_021947) Copy   

•   Source: SciCrunch Registry
  

https://github.com/mbillingr/libgdf

Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - " general dataformat for biosignals" version V2.20.

Proper citation: libGDF (RRID:SCR_024075) Copy   

•   Source: SciCrunch Registry
  

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
  

https://edspace.american.edu/openbehavior/project/self-grooming-mice/

Portal provides protocol that implements JAABA, open source machine learning based behavior detection system; motr, open-source mouse trajectory tracking software; and bonsai, open source system capable of streaming and recording video. Together they use these tools to process videos of mice performing grooming behaviors in variety of behavioral setups.

Proper citation: Automated Classification of Self-grooming in Mice project (RRID:SCR_021597) Copy   

•   Source: SciCrunch Registry
  

https://lincsportal.ccs.miami.edu/signatures/home

Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.

Proper citation: LINCS Data Portal 2.0 (RRID:SCR_022566) 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://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/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://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
  

https://github.com/humanlongevity/HLA

Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.

Proper citation: xHLA (RRID:SCR_022277) Copy   

•   Source: SciCrunch Registry
  

https://www.biocompare.com/19333-Image-Analysis-Software-Image-Processing-Software/4378970-Definiens-Tissue-Studio/

Software to detect regions of interests and distinguishes cells and sub-cellular objects within these target regions from immunohistochemistry specimen. Used for digital pathology image analysis.

Proper citation: Tissue Studio (RRID:SCR_023001) Copy   

•   Source: SciCrunch Registry
  

https://bbp.epfl.ch/nmc-portal/welcome.html

Neocortical microcircuit collaboration portal is resource for rat somatosensory cortex. NMC portal allows users to access experimental data used in reconstruction process, download cellular and synaptic models, and analyze predicted properties of microcircuit.

Proper citation: Neocortical Microcircuit Portal (RRID:SCR_022032) Copy   

•   Source: SciCrunch Registry
  

https://www.cis.jhu.edu/~younes/CA.html

Web portal that explains technique of Diffeomorphic Mapping and Shape Analysis.

Proper citation: Generative Diffeomorphic Mapping (RRID:SCR_022825) Copy   

•   Source: SciCrunch Registry
  

http://www.psc.edu/

Joint computational research center with Carnegie Mellon University and University of Pittsburgh. Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research.

Proper citation: Pittsburgh Supercomputing Center (RRID:SCR_022823) Copy   

•   Source: SciCrunch Registry
  

https://github.com/vesselman/SparkAn

Software tool for custom calcium imaging analysis.

Proper citation: SparkAn (RRID:SCR_022028) Copy   

•   Source: SciCrunch Registry
  

https://rewireneuro.com/product/pipsqueak/

Software image analysis tool as older ImageJ/Fiji plugin version.

Proper citation: Pipsqueak AI (RRID:SCR_022149) Copy   

•   Source: SciCrunch Registry
  

https://github.com/Kingsford-Group/kourami

Software graph guided assembly for novel human leukocyte antigen allele discovery. Graph guided assembly for HLA haplotypes covering typing exons using high coverage whole genome sequencing data.Implemented in Java and supported on Linux and Mac OS X.

Proper citation: Kourami (RRID:SCR_022280) Copy   

•   Source: SciCrunch Registry