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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Platform for individuals who want to make their own data available for research. Used by people to join network with others who wish to contribute to vital research in partnership with and alongside leading scientists. Personal tool for saving and displaying medical information.
Proper citation: Hugo Data (RRID:SCR_022763) Copy
https://github.com/linnarsson-lab/loom-viewer
Software tool for sharing, browsing and visualizing single-cell data stored in the Loom file format.
Proper citation: loom-viewer (RRID:SCR_016683) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy
Integrated healthcare biobank that operates under certified conditions and strict SOPs. Enables biomedical and translational researchers to perform their analyses using high quality biospecimens and data to generate reliable and reproducible research data. Core offers modular biobanking portfolio that can cover workflow from blood collection to storage, including all pre-analytical steps and their documentation. Offers spectrum of additional services ranging from DNA/RNA extraction and virtual microscopy to entire management of sample and data flow for national and international research consortia. Provides secure conventional and automated storage of samples at various temperatures as well as secure data management.
Proper citation: Charite University and Berlin Institute for Health Research Central Biobank Core Facility (RRID:SCR_023495) Copy
Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.
Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy
https://rubygems.org/gems/viral_seq
Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis.
Proper citation: viral_seq (RRID:SCR_018515) Copy
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
Brainarray custom CDFs for processing raw Affymetrix data. Used to map probe to probesets. Oligonucleotide probes on GeneChips are reorganized based on latest genome and transcriptome information.
Proper citation: CustomCDF (RRID:SCR_018527) Copy
A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.
Proper citation: MS Bioworks (RRID:SCR_001043) Copy
http://www.worm.mpi-cbg.de/phenobank/cgi-bin/ProjectInfoPage.py
A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens.
Proper citation: PhenoBank (RRID:SCR_000930) Copy
https://github.com/sanger-pathogens/Bio-Tradis
Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.
Proper citation: Bio-tradis (RRID:SCR_015993) Copy
https://github.com/ABCD-STUDY/FIONASITE
Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive.
Proper citation: FIONASITE (RRID:SCR_016012) Copy
https://github.com/ABCD-STUDY/Minimally-Processed-Image-Sharing
Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository.
Proper citation: Minimally-Processed-Image-Sharing (RRID:SCR_016016) Copy
https://github.com/ABCD-STUDY/Fast-Track-Image-Sharing
Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA).
Proper citation: Fast-Track-Image-Sharing (RRID:SCR_016021) Copy
https://github.com/ABCD-STUDY/eprime-data-clean
Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests.
Proper citation: eprime-data-clean (RRID:SCR_016020) Copy
Software for DNA and amino acid editing, database management, plasmid maps, It can also be used for restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
Proper citation: Gentle (RRID:SCR_016127) Copy
http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Bio++ (RRID:SCR_016055) Copy
https://github.com/thegenemyers/DAZZ_DB
Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.
Proper citation: Dazzler (RRID:SCR_016069) Copy
https://github.com/ABCD-STUDY/DEAP
Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.
Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy
https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html
Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.
Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy
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