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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.
https://github.com/cwatson/braingraph/
Software R package for performing graph theory analyses of brain MRI data.
Proper citation: brainGraph (RRID:SCR_017260) Copy
https://github.com/drchrisch/SynapseLocator
Software tool that combines steps of image processing, non rigid image registration, and spot localisation. Performs registration of 3D imaging data and localization of spots, active synapses in light microscopy images, in semi automatic mode with graphical user interface.
Proper citation: SynapseLocator (RRID:SCR_017263) Copy
https://ous-research.no/bioinformatics/
Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services.
Proper citation: Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) Copy
Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging.
Proper citation: Mass spectrometry imaging workbench (RRID:SCR_017410) Copy
https://github.com/zuoxinian/CCS
Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.
Proper citation: Connectome Computation System (RRID:SCR_017342) Copy
Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are.
Proper citation: miRpathDB (RRID:SCR_017356) Copy
https://rdrr.io/github/LTLA/batchelor/man/fastMNN.html
Software tool to correct for batch effects in single-cell expression data using fast version of mutual nearest neighbors (MNN) method.
Proper citation: fastMNN (RRID:SCR_017351) Copy
https://github.com/biocore/redbiom
Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data.
Proper citation: redbiom (RRID:SCR_017285) Copy
http://bio3d.colorado.edu/SerialEM/
Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function.
Proper citation: SerialEM (RRID:SCR_017293) Copy
Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms.
Proper citation: SynGO (RRID:SCR_017330) Copy
https://www.beilstein-strenda-db.org/strenda/
Storage and search platform supported by Beilstein-Institut that incorporates STRENDA Guidelines. For authors who prepare manuscript containing functional enzymology data, STRENDA DB provides means to ensure that data sets are complete and valid before submitting them to journal.
Proper citation: STRENDA (RRID:SCR_017422) Copy
Medical image repository to store medical research data.
Proper citation: SICAS Medical Image Repository (RRID:SCR_017420) Copy
https://beast.community/tempest
Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019.
Proper citation: TempEst (RRID:SCR_017304) Copy
Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser.
Proper citation: European Variation Archive (EVA) (RRID:SCR_017425) Copy
https://software.broadinstitute.org/morpheus/
Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis.
Proper citation: Morpheus by Broad Institute (RRID:SCR_017386) Copy
http://www.biomexsolutions.co.uk/morda
Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline.
Proper citation: MoRDa (RRID:SCR_017278) Copy
http://clustalw.ddbj.nig.ac.jp/index.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan.
Proper citation: ClustalW (RRID:SCR_017277) Copy
http://www.brainimagelibrary.org
Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets.
Proper citation: Brain Image Library (RRID:SCR_017272) Copy
https://www.qiagenbioinformatics.com/products/clc-genomics-server/
Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler.
Proper citation: CLC Genomics Server (RRID:SCR_017396) Copy
Software tool for practical self assessment and reporting method for clinical research studies, to capture key information about data acquisition and quality control measures. Linked to dataset so that potential research collaborators can determine if data meets their needs and expectations.
Proper citation: DAQCORD (RRID:SCR_017395) Copy
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