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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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KaleidaGraph Resource Report Resource Website 1000+ mentions |
KaleidaGraph (RRID:SCR_014980) | data analysis software, data processing software, data visualization software, software application, software resource | Data analysis, graphing, and management application that allows users to import, manipulate, analyze data, and create customized plots. Plots include x-y probability, histogram, box, percentile, horizontal bar, stack bar, column, stack column, polar, and pie. Binned data can be exported to a histogram, step plot, or spike plot. KaleidaGraph works with Windows and Macintosh systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | custom graph, custom plot, publishable graph, publishable plot, data manipulation, curve fitting | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014980 | SciCrunch Registry | 2026-10-31 12:16:28 | 2789 | ||||||||||
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BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. | cluster, protein, nucleotide, sequence, pairwise, match, sequence |
is listed by: SoftCite has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | SCR_016641 | SciCrunch Registry | 2026-10-31 12:16:51 | 94 | ||||||||||
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CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | data analysis software, data processing software, software application, software resource | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | SciCrunch Registry | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-10-31 12:16:41 | 114 | ||||||||
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EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | SciCrunch Registry | EMAN1, EMAN2 | 2026-10-31 12:16:42 | 107 | |||
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CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | data analysis software, data processing software, software application, software resource | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | SciCrunch Registry | CFX Manager software | 2026-10-31 12:16:57 | 492 | |||||||||
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RNAstructure Resource Report Resource Website 50+ mentions |
RNAstructure (RRID:SCR_017216) | analysis service resource, data access protocol, production service resource, service resource, simulation software, software application, software resource, web service | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | SciCrunch Registry | 2026-10-31 12:16:48 | 58 | ||||||||
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ClustalW Resource Report Resource Website 10000+ mentions |
ClustalW (RRID:SCR_017277) | ClustalW of DDBJ | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan. | alignment, service, DNA, data, bank, Japan | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017277 | SciCrunch Registry | ClustalW of DNA Data Bank of Japan | 2026-10-31 12:16:50 | 10545 | ||||||||
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Rhinoceros Resource Report Resource Website 100+ mentions |
Rhinoceros (RRID:SCR_014339) | simulation software, software application, software resource, standalone software | 3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products. | 3d, modeling software, standalone software | is listed by: SoftCite | Pay for product | SCR_014339 | SciCrunch Registry | Rhino | 2026-10-31 12:19:17 | 311 | |||||||||
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STRUCTURE Resource Report Resource Website 1000+ mentions |
STRUCTURE (RRID:SCR_017637) | software resource, software toolkit | Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms. | Multi locus genotype data, investigate population structure, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: STRAT has parent organization: Stanford University; Stanford; California works with: Structure Harvester |
PMID:21564903 PMID:18784791 PMID:12930761 PMID:10835412 |
Free, Available for download, Freely available | SCR_021634, nlx_154662, SCR_002151, biotools:structure | https://bio.tools/structure, http://pritch.bsd.uchicago.edu/structure.html, | SCR_017637 | SciCrunch Registry | structure, Structure | 2026-10-31 12:19:22 | 4177 | ||||||
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Argus Resource Report Resource Website 1+ mentions |
Argus (RRID:SCR_021585) | data or information resource, portal, project portal, software resource | Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior. | Analysis, quantification, socially interacting zebrafish, OpenBehavior |
is listed by: OpenBehavior is listed by: SoftCite is related to: Argus |
DOI:10.3758/s13428-018-1083-y | Free, Freely available | SCR_021619 | SCR_021585 | SciCrunch Registry | 2026-10-31 12:19:29 | 1 | ||||||||
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GeneTools Resource Report Resource Website 100+ mentions |
GeneTools (RRID:SCR_022505) | data processing software, image analysis software, software application, software resource | Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting. | Synoptics Ltd., Syngene, chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging, colony counting. | is listed by: SoftCite | Restricted | SCR_022505 | SciCrunch Registry | 2026-10-31 12:19:30 | 201 | ||||||||||
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GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | SciCrunch Registry | Generic Genome Browser | 2026-10-31 12:20:22 | 43 | ||||
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piRNABank Resource Report Resource Website 100+ mentions |
piRNABank (RRID:SCR_007858) | data or information resource, database | A web analysis system and resource, which provides comprehensive information on piRNAs in the widely studied mammals. It compiles all the possible clusters of piRNAs and also depicts piRNAs along with the associated genomic elements like genes and repeats on a genome wide map. piRNABank mainly provides data onnamely Human, Mouse, Rat, Zebrafish, Platypus and a fruit fly, Drosophila.Search options have been designed to query and obtain useful data from this online resource. It also facilitates abstraction of sequences and structural features from piRNA data. piRNABank provides the following features: * Simple search * Search piRNA clusters * Search homologous piRNAs * piRNA visualization map * Analysis tools, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03293 | SCR_007858 | SciCrunch Registry | piRNABank | 2026-10-31 12:20:26 | 172 | ||||||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
Canadian Foundation for Innovation ; Canadian Institutes for Health Research ; Michael Smith Foundation for Health Research ; NIGMS GM076990 |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/, https://doi.org/10.17616/R36R54, https://doi.org/10.17616/R36R54 | SCR_008007 | SciCrunch Registry | 2026-10-31 12:20:29 | 1145 | |||||
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Ingenuity Pathways Knowledge Base Resource Report Resource Website 1000+ mentions |
Ingenuity Pathways Knowledge Base (RRID:SCR_008117) | data or information resource, database | A horizontally and vertically structured database that pulls scientific and medical information and describes it consistently using the Ingenuity Ontology. The Knowledge Base pulls information from journals, public molecular content databases, and textbooks. Data is curated and and integrated into the Knowledge Base . | gene, life science, molecule, protein, research, software, ontology, knowledge base, FASEB list |
is used by: Ingenuity Pathway Analysis is listed by: SoftCite has parent organization: QIAGEN |
Available to the research community, Commercial | nif-0000-20858 | SCR_008117 | SciCrunch Registry | Ingenuity Knowledge Base | 2026-10-31 12:20:36 | 4808 | ||||||||
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jcvi Resource Report Resource Website 10+ mentions |
jcvi (RRID:SCR_021641) | software library, software resource, software toolkit | Software tool as collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Python libraries, parse bioinformatics files, assembly, annotation, comparative genomics | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tanghaibao/jcvi/tree/v0.5.7, https://zenodo.org/record/31631#.YRaieYhKhPa | SCR_021641 | SciCrunch Registry | jcvi_PyPI, jcvi 1.1.17 | 2026-10-31 12:18:22 | 20 | ||||||||
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TreeBASE Resource Report Resource Website 500+ mentions |
TreeBASE (RRID:SCR_005688) | TreeBASE | data or information resource, data repository, database, service resource, storage service resource | Repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all kinds of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Data used in publications that are in preparation or in review can be submitted to TreeBASE but will not be available to the public until they have passed peer review. | taxonomy, matrix, tree, topology, phylogeography, cladistic analysis, amino acid sequence, animal behavior, morphology, nucleotide sequence, genetics, dna, phylogeny, evolution, gene, population, web service, FASEB list |
is listed by: re3data.org is listed by: SoftCite has parent organization: NESCent - National Evolutionary Synthesis Center |
NSF DEB 9318325; NSF EF 0331654 |
Public, The community can contribute to this resource | r3d100010170, nif-0000-03587 | https://doi.org/10.17616/R3DK58 | SCR_005688 | SciCrunch Registry | TreeBASE - A Database of Phylogenetic Knowledge | 2026-10-31 12:18:29 | 813 | |||||
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SPM Resource Report Resource Website 5000+ mentions Issue |
SPM (RRID:SCR_007037) | SPM | data analysis software, data processing software, image analysis software, software application, software resource | Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. | analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools |
uses: Neuroimaging Data Model uses: imcalc: SPM batch image calculator is used by: rsfMRI_fconn calculation is used by: Automatic Analysis is used by: auto_acpc_reorient is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite is affiliated with: Clinical Toolbox for SPM is affiliated with: Statistical non-Parametric Mapping is related to: WFU Biological Parametric Mapping Toolbox is related to: vis: SPM Visualized Statistics toolbox is related to: LEAD-DBS is related to: CCHMC Pediatric Brain Templates is related to: IBMA toolbox is related to: ArtRepair for robust fMRI is related to: ASL data processing tool box is related to: BrainVISA / Anatomist is related to: MRIcro Software is related to: xjView: A Viewing Program For SPM is related to: BrainMagix SPM Viewer is related to: MarsBaR region of interest toolbox for SPM is related to: NIRS-SPM is related to: SPM SS - fMRI functional localizers is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox is related to: Dementia-specific FDG PET Template for SPM analyses is related to: SPM Anatomy Toolbox is related to: MIPAV: Medical Image Processing and Visualization is related to: MATLAB is related to: hMRI-toolbox is related to: Sandwich Estimator Toolbox has parent organization: University College London; London; United Kingdom is required by: MRTool provides: TSDiffAna has plug in: ICN_Atlas works with: UManitoba - JHU Functionally Defined Human White Matter Atlas works with: NIAG Addiction Data works with: ICN_Atlas works with: spm_auto_reorient_coregister works with: Computational Anatomy Toolbox for SPM works with: FieldTrip works with: POAS4SPM |
Free, Available for download, Freely available | biotools:SPM | https://github.com/spm/spm12, https://bio.tools/SPM | https://www.fil.ion.ucl.ac.uk/spm/ | SCR_007037 | SciCrunch Registry | Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 | 2026-10-31 12:18:36 | 8748 | |||||
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MUSCLE Resource Report Resource Website 10000+ mentions |
MUSCLE (RRID:SCR_011812) | MUSCLE | alignment software, analysis service resource, data analysis service, data analysis software, data processing software, image analysis software, production service resource, service resource, software application, software resource | Multiple sequence alignment method with reduced time and space complexity.Multiple sequence alignment with high accuracy and high throughput. Data analysis service for multiple sequence comparison by log- expectation. | bio.tools |
is used by: TranslatorX is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: PREFAB has parent organization: European Bioinformatics Institute |
PMID:15034147 PMID:15318951 DOI:10.1093/nar/gkh340 |
biotools:muscle, OMICS_00982 | https://bio.tools/muscle, http://www.drive5.com/muscle/, https://www.drive5.com/muscle/manual/, https://www.drive5, http://bioconductor.org/packages/release/bioc/html/muscle.html.com/muscle/manual/install.html, https://sources.debian.org/src/muscle/ | SCR_011812 | SciCrunch Registry | MUltiple Sequence Comparison by Log- Expectation | 2026-10-31 12:18:28 | 17169 | ||||||
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CLC Genomics Workbench Resource Report Resource Website 100+ mentions |
CLC Genomics Workbench (RRID:SCR_011853) | data analysis software, data processing software, data visualization software, software application, software resource | Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program. | ngs, next, generation, sequencing, gene, rna, visualisation, analysis |
is listed by: OMICtools is listed by: SoftCite works with: CLC Genomics Server |
Restricted | SCR_016245, OMICS_01124 | SCR_011853 | SciCrunch Registry | 2026-10-31 12:18:34 | 187 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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