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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Gene Expression Profile Analysis Suite Resource Report Resource Website 10+ mentions |
Gene Expression Profile Analysis Suite (RRID:SCR_008341) | software application, data processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. | expression, gene, analysis, genomic, microarray, microarray platform, prediction, data set |
is listed by: 3DVC has parent organization: Principe Felipe Research Centre; Valencia; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25201 | SCR_008341 | Gepas | 2026-02-17 10:01:07 | 20 | ||||||||
|
CURRY Resource Report Resource Website 100+ mentions |
CURRY (RRID:SCR_009546) | CURRY | software application, data processing software, software resource | Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package. | multimodal, atlas, application, connectivity, analysis, computed, tomography, database, eeg, meg, electrocorticography, modeling, finite, element, format, conversion, forward, inverse, image, reconstruction, meg, mesh, generation, model, magnetic resonance, pet, spect, segmentation, simulation, spatial, transformation, volumetric, neuroimaging, FASEB list | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155726 | http://www.nitrc.org/projects/curry_7 | SCR_009546 | CURRY Scan 7 Neuroimaging Suite, CURRY 8, CURRY 7, CURRY Neuroimaging Suite | 2026-02-17 10:01:31 | 160 | ||||||
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MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | software application, data processing software, software resource, software toolkit | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2026-02-17 10:01:14 | 1266 | ||||||
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Template Based Rotation Resource Report Resource Website 1+ mentions |
Template Based Rotation (RRID:SCR_012157) | TBR | image analysis software, software application, data processing software, software resource | A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations. | functional connectivity, analysis, fmri, fcmri, parcellation, map, template, resting state, matlab | Aging | NIA P01AG036694 | DOI:10.1016/j.neuroimage.2014.08.022 | GNU General Public License v3 | rid_000095 | http://nmr.mgh.harvard.edu/harvardagingbrain/People/AaronSchultz/Aarons_Scripts.html | SCR_012157 | Template Based Rotation (TBR) | 2026-02-17 10:01:40 | 1 | ||||
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Open Babel Resource Report Resource Website 50+ mentions |
Open Babel (RRID:SCR_014920) | software application, data processing software, software resource, data analytics software | Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats. | toolbox, conversion, analysis, molecular model, chemistry, biochemistry, chemical file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:open_babel | https://bio.tools/open_babel | SCR_014920 | 2026-02-17 10:02:45 | 81 | ||||||||
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Center for Computational Biology at JHU Resource Report Resource Website 1+ mentions |
Center for Computational Biology at JHU (RRID:SCR_016680) | CCB at JHU | data or information resource, portal, organization portal | Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis. | center, computational, biology, genomics, genetics, DNA, RNA, sequence, technology, analysis |
has parent organization: Johns Hopkins University; Maryland; USA is parent organization of: Centrifuge Classifier |
SCR_016680 | CCB at Johns Hopkins University, CCB at JHU, Center for Computational Biology at JHU, Center for Computational Biology at Johns Hopkins University | 2026-02-17 10:03:27 | 1 | |||||||||
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ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | data or information resource, portal, organization portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-02-17 10:03:15 | 12 | ||||||
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Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | image analysis software, software application, data processing software, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-02-17 10:03:22 | 13 | ||||||
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SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | image analysis software, software application, data processing software, software resource | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | NIH ; NLM ; LHNCBC HHSN276201500692P |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-02-17 10:03:22 | 4 | |||||||||
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cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | image analysis software, software application, data processing software, software resource | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-02-17 10:03:27 | 2480 | |||||||||
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BZ-H3A analyzer software Resource Report Resource Website 10+ mentions |
BZ-H3A analyzer software (RRID:SCR_017375) | image analysis software, software application, data processing software, software resource | Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series. | Analysis, Keyence, Japan, fluorescence, microscope, BZ-X | SCR_017375 | 2026-02-17 10:02:51 | 10 | ||||||||||||
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Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, data processing software, software resource | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-02-17 10:02:54 | 59 | ||||||
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Image Quant TL Resource Report Resource Website 100+ mentions |
Image Quant TL (RRID:SCR_018374) | image analysis software, software application, data processing software, software resource | Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting. | Image analysis, Cytiva, image, electrophoresis gel image, blot image, array, colony count image, analysis | SCR_018374 | , Image Quant TL array analysis, ImageQuant TL 8.2 | 2026-02-17 10:03:28 | 381 | |||||||||||
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UN-SCAN-IT Gel Analysis Software Resource Report Resource Website 1+ mentions |
UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) | image analysis software, software application, data processing software, software resource | Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC. | electrophoresis, gel, image, analysis, density, quantification, Silk Scientific Inc | Restricted | SCR_017291 | 2026-02-17 10:02:50 | 9 | |||||||||||
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Stereo Investigator - Whole Slide Edition Resource Report Resource Website 1+ mentions |
Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) | image analysis software, software application, data processing software, software resource | Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses. | Quantitative, analysis, stereology, whole, slide, image, MBF Bioscience | Restricted | SCR_017667 | 2026-02-17 10:03:17 | 3 | |||||||||||
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HALO Resource Report Resource Website 50+ mentions |
HALO (RRID:SCR_018350) | HALO | image analysis software, software application, data processing software, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-02-17 10:03:04 | 77 | ||||||||
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IncuCyte® Chemotaxis Software Resource Report Resource Website 10+ mentions |
IncuCyte® Chemotaxis Software (RRID:SCR_017316) | image analysis software, software application, data processing software, software resource | IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate. | Add-on, module, IncuCyte ZOOM, live-cell, analysis, system, ClearView, Chemotaxis, Plate, Essen Bioscience, Sartorius | is provided by: Sartorius | Restricted | SCR_017316 | IncuCyte Chemotaxis Software | 2026-02-17 10:03:34 | 11 | |||||||||
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cwl-metrics Resource Report Resource Website 1+ mentions |
cwl-metrics (RRID:SCR_017076) | CWL-metrics | software library, software resource, software toolkit | Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux. | collect, analyze, computational, resource, usage, workflow, common, language, container, cloud, data, analysis | is listed by: OMICtools | Japan Science and Technology Agency | DOI:10.1101/456756 | Free, Available for download, Freely available | OMICS_32746 | SCR_017076 | Common Workflow Language-metrics, common workflow language metrix | 2026-02-17 10:03:31 | 1 | |||||
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Mayo Clinic Rochehster Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
Mayo Clinic Rochehster Bioinformatics Core Facility (RRID:SCR_017161) | Mayo Clinic Bioinformatics Core | production service resource, analysis service resource, access service resource, core facility, service resource, data analysis service | Core assists in genomics, proteomics and metabolomics data acquisition, management, analyses and interpretation to Mayo investigators. Participates in Basic science research, Clinical trials, Population health, and Translational science to execute analytical workflows and manage large omics data sets. Provides support to Mayo Clinic Center for Individualized Medicine and Mayo Clinic Cancer Center. Has its academic home in Department of Health Sciences Research within Division of Biomedical Statistics and Informatics. | bioinformatics, data, acquisition, management, analysis, genomics, proteomics, metabolomics | has parent organization: Mayo Clinic | Restricted | SCR_017161 | Bioinformatics Core, Division of Biomedical Statistics and Informatics, Rochehster, Mayo Clinic, Core Facility | 2026-02-17 10:03:31 | 2 | ||||||||
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Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility Resource Report Resource Website |
Max Planck Institiute of Immunobiology and Epigenetics Bioinformatics Core Facility (RRID:SCR_017160) | production service resource, analysis service resource, access service resource, service resource, software resource, core facility, data analysis service | Core provides assistance in primary analysis of sequencing data and other large scale biocomputing. For our internal users we host extensive web services, workflows and customized tools that help with data management, visualizations, standardized analyses and data sharing. | bioinformatics, biocomputing, sequencing, data, omics, analysis, visualization, management | has parent organization: Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany | Restricted | SCR_017160 | , Bioinformatics Facility, Core Facility, Bioinformatics Core Facility, Epigenetics, Max Planck Institiute of Immunobiology | 2026-02-17 10:03:10 | 0 |
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