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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AmplifX Resource Report Resource Website 50+ mentions |
AmplifX (RRID:SCR_014465) | data analysis software, data processing software, software application, software resource | A software for managing, testing, and drawing primers. The software can locate primers for target sequences, calculate the quality score, predict amplified fragments and dimers, and create graphic representations of the primers. | primer design, target sequences, amplification, graphic representation, data analysis software | SCR_014465 | SciCrunch Registry | 2026-09-26 02:17:12 | 96 | ||||||||||||
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Scaffold Proteome Software Resource Report Resource Website 100+ mentions |
Scaffold Proteome Software (RRID:SCR_014345) | data analysis software, data processing software, software application, software resource | Software for MS/MS proteomic experiments to compare samples, identify biological relevance, and identify isoforms and protein PTMs. These proteins can be classified based on molecular function or organelle. Users can investigate spectrum details and counts, as well as use high through-put batch processing. Tutorials and a free trial are available through the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ms/ms, proteome, isoform, protein ptm, spectrum, mass spectrometry | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014345 | SciCrunch Registry | Scaffold | 2026-09-26 02:17:12 | 116 | ||||||||||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | data or information resource, database, portal, project portal, software resource, web application | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | SciCrunch Registry | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-09-26 02:17:13 | 20 | |||||||
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PLEXdb - Plant Expression Database Resource Report Resource Website 10+ mentions |
PLEXdb - Plant Expression Database (RRID:SCR_006963) | PLEXdb | analysis service resource, data analysis service, data or information resource, data repository, database, portal, production service resource, service resource, storage service resource, topical portal | PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets. | gene expression, plant, plant pathogen, genotype, phenotype, genetic, physical, pathway, plant biology, compare, functional genomics, expression profiling, expression atlas, pathogen, genome, anova, cluster, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: FuncExpression has parent organization: Iowa State University; Iowa; USA |
UniNSF DBI-0543441; NSF IOS-0922746; USDA 3625-21000-049-00D |
PMID:22084198 | biotools:plexdb, r3d100011516, nlx_149236 | https://bio.tools/plexdb, https://doi.org/10.17616/R39D13 | SCR_006963 | SciCrunch Registry | PLEXdb - Gene expression resources for plants and plant pathogens, Plant Expression Database | 2026-09-26 02:17:09 | 21 | |||||
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HDBase Resource Report Resource Website |
HDBase (RRID:SCR_007132) | HDBase | data or information resource, data set, disease-related portal, portal, topical portal | A community website for Huntington''s Disease (HD) research that currently contains Y2H and Mass spectrometry protein-protein interaction data centered around the HD protein (huntingtin) and information on therapeutic studies in mouse. Also available are raw Human and Mouse Affymetrix Microarray data. The protein interaction data is from several sources, including interactions curated from the literature by ISB staff, experimentally determined interactions produced by Bob Hughes and colleagues at Prolexys (currently password protected), and interactions reported in a recent publication by Goehler et al from Eric Wanker''s lab. Content areas that may be covered by the site include the following: * Therapeutic studies in mouse, primarily drug screens. * HD mouse models with a focus on timelines of disease progression. * Antibodies used in HD research. * Microarray gene expression studies. * Genes and proteins relevant to HD research. This includes HD itself, the growing list of proteins thought to interact directly or indirectly with huntingtin (Htt), and other genes and proteins implicated in the disease process. * Molecular pathways thought to be involved in the disease process. * Timelines of disease for Mouse models | drug, gene expression, huntingtin, mass spectrometry, microarray, protein interaction, protein-protein interaction, y2h, mouse model, treatment, disease, phenotype, brain, striatum, adipose, muscle, gene, protein, antibody, pathway |
uses: Cytoscape has parent organization: Institute for Systems Biology; Washington; USA |
Huntington''s disease, Control | Hereditary Disease Foundation | nif-0000-00153 | SCR_007132 | SciCrunch Registry | HDBase - A Community Website for Huntingtons Disease Research, HDBase - A Community Website for Huntington''s Disease Research | 2026-09-26 02:17:09 | 0 | ||||||
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Cytoseg Resource Report Resource Website 1+ mentions |
Cytoseg (RRID:SCR_009553) | Cytoseg | data processing software, image analysis software, segmentation software, software application, software resource | A tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. It works best for 3D blob shaped objects like mitochondria, lysosomes, etc. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools). | computational neuroscience, neuropil, 3d electron microscopy, electron microscopy | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU Lesser General Public License | nlx_155733 | http://www.nitrc.org/projects/cytoseg | SCR_009553 | SciCrunch Registry | 2026-09-26 02:17:10 | 1 | |||||||
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University of Arkansas for Medical Sciences Department of Pharmacology and Toxicology Resource Report Resource Website |
University of Arkansas for Medical Sciences Department of Pharmacology and Toxicology (RRID:SCR_007496) | data or information resource, department portal, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 25,2022. Department of Pharmacology and Toxicology is the professional home to 18 faculty, 11 research faculty, 22 graduate students and 3 postdoctoral fellows. They offer graduate training leading to the Ph.D. degree in Pharmacology or Interdisciplinary Toxicology. Their faculty also participate in the Interdisciplinary Biological Sciences (IBS) training programs. Trainees receive a broad-based education to prepare for a career in translational research. An emphasis on therapeutic development, identification of drug targets and mechanisms of organ injury prepare our trainees for a career in drug discovery and medical toxicology. All of our students currently receive a $24,000 yearly stipend and we pay tuition! Their 'magnet areas' for research include behavioral and drug abuse pharmacology, drug discovery and antibody therapeutics, mechanisms and therapies of organ toxicology and neurodegenerative diseases, and CNS and vascular ion channels. Extramural research funding obtained by the faculty has increased to more than 5 million annually, and the Department ranks in the top quarter of all medical school pharmacology departments in the country in NIH funding. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02134 | SCR_007496 | SciCrunch Registry | UAMS | 2026-09-26 02:17:12 | 0 | ||||||||||
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ASaiM Resource Report Resource Website 1+ mentions |
ASaiM (RRID:SCR_015878) | data analysis software, data processing software, software application, software resource | Software that analyzes intestinal microbiota data. This environment is composed of a framework to process and analyze microbiota data from raw sequences to taxonomic and functional assignations. | metagenomic, galaxy, microbiota, metatranscriptomic, metataxonomic, | Open source, Free, Available for download, Tutorial available | https://github.com/asaim | SCR_015878 | SciCrunch Registry | ASaiM: Auvergne Sequence analysis of intestinal Microbiota, Auvergne Sequence analysis of intestinal Microbiota, ASaiM (Auvergne Sequence analysis of intestinal Microbiota) | 2026-09-26 02:17:17 | 2 | |||||||||
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Michigan State University Labs and Facilities Resource Report Resource Website |
Michigan State University Labs and Facilities (RRID:SCR_012252) | MSU Labs & Facilities, MSU Labs and Facilities | access service resource, core facility, data or information resource, portal, service resource | An Portal, Core facility |
is listed by: ScienceExchange is related to: Michigan State University RTSF Genomics Core Facility is related to: MSU Comprehensive Phytopathogen Genomics Resource has parent organization: Michigan State University; Michigan; USA |
SciEx_1277 | SCR_012252 | SciCrunch Registry | Michigan State University Labs & Facilities | 2026-09-26 02:17:11 | 0 | |||||||||
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Digital Fish Library Resource Report Resource Website |
Digital Fish Library (RRID:SCR_008338) | DFL | data or information resource, database, image collection, training resource | A database of 3D magnetic resonance (MRI) images of fish accessible to scientists, educators and the general public via the web. The Marine Vertebrate Collection at the Scripps Institution of Oceanography provides the majority of the DFL specimens. | education, fish, 3d, anatomical, magnetic resonance imaging, marine, mri, oceanography, comparative anatomy | has parent organization: University of California at San Diego; California; USA | NSF DBI-0446389 | nif-0000-24963 | SCR_008338 | SciCrunch Registry | DFL - Digital Fish Library | 2026-09-26 02:17:10 | 0 | |||||||
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Fiber Tracking / DTI Checker Resource Report Resource Website |
Fiber Tracking / DTI Checker (RRID:SCR_007364) | data analysis software, data processing software, software application, software resource | A cross-platform system for exploring diffusion tensor images and to reconstruct fiber tracts between two regions of interest, intended for tdoctors, medical technicians or medical researchers. The Fiber-Tracking tool allows the user to load data from MRIs or similar images (like a basic 3D image viewer), load DTI datasets (7 diffusion- weighted images), calculate the fractional anisotropy (FA) and the mean diffusivity (MD) images, and also load ROIs to reconstruct fibers. | diffusion tensor imaging, tractography | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | nif-0000-00299 | http://www.ia.unc.edu/dev/download/fibertracking/index.htm, http://www.ia.unc.edu/dev/download/dtichecker/index.htm | http://www.ia.unc.edu/dev/download/index.htm | SCR_007364 | SciCrunch Registry | Fiber Tracking | 2026-09-26 02:17:09 | 0 | |||||||
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Genetic and Rare Diseases Information Center Resource Report Resource Website 10+ mentions |
Genetic and Rare Diseases Information Center (RRID:SCR_008695) | GARD | data or information resource, disease-related portal, portal, topical portal | Genetic and Rare Diseases Information Center (GARD) is a collaborative effort of two agencies of the National Institutes of Health, The Office of Rare Diseases Research (ORDR) and the National Human Genome Research Institute (NHGRI) to help people find useful information about genetic conditions and rare diseases. GARD provides timely access to experienced information specialists who can furnish current and accurate information about genetic and rare diseases. So far, GARD has responded to 27,635 inquiries on about 7,147 rare and genetic diseases. Requests come not only from patients and their families, but also from physicians, nurses and other health-care professionals. GARD also has proved useful to genetic counselors, occupational and physical therapists, social workers, and teachers who work with people with a genetic or rare disease. Even scientists who are studying a genetic or rare disease and who need information for their research have contacted GARD, as have people who are taking part in a clinical study. Community leaders looking to help people find resources for those with genetic or rare diseases and advocacy groups who want up-to-date disease information for their members have contacted GARD. And members of the media who are writing stories about genetic or rare diseases have found the information GARD has on hand useful, accurate and complete. GARD has information on: :- What is known about a genetic or rare disease. :- What research studies are being conducted. :- What genetic testing and genetic services are available. :- Which advocacy groups to contact for a specific genetic or rare disease. :- What has been written recently about a genetic or rare disease in medical journals. GARD information specialists get their information from: :- NIH resources. :- Medical textbooks. :- Journal articles. :- Web sites. :- Advocacy groups, and their literature and services. :- Medical databases. | genetic, disease, information, genome, human, rare disease, health, physician, counselor, gene, journal, medical | has parent organization: National Institutes of Health | Office of Rare Diseases Research ; NHGRI |
nif-0000-37627 | SCR_008695 | SciCrunch Registry | Genetic Rare Diseases Information Center | 2026-09-26 02:17:10 | 16 | |||||||
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SUNY Stony Brook, Pharmacological Sciences Resource Report Resource Website |
SUNY Stony Brook, Pharmacological Sciences (RRID:SCR_007480) | data or information resource, department portal, organization portal, portal | The Department ofPharmacological Sciencesat Stony Brook offers a collegial atmosphere with one of the highest ratios of postdoctoral to predoctoral researchers of any Pharmacology Department in the country. Students in Molecular and Cellular Pharmacology work alongside students from several other graduate programs at Stony Brook, including Molecular and Cellular Biology, Neurobiology, Chemistry, Genetics, Microbiology, Structural Biology, and Physiology and Biophysics. Several students in Molecular and Cellular Pharmacology have been trainees in the NIH-funded MSTP (Medical Scientist Training Program). | nif-0000-02081 | SCR_007480 | SciCrunch Registry | SUNY Stonybrook | 2026-09-26 02:17:09 | 0 | |||||||||||
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ImmunoStar Resource Report Resource Website 500+ mentions |
ImmunoStar (RRID:SCR_013473) | antibody supplier, commercial organization, material resource, reagent supplier | An Antibody supplier | nlx_152388 | SCR_013473 | SciCrunch Registry | Immunonuclear, Diasorin, Incstar, Immuno Nuclear, ImmunoStar inc. | 2026-09-26 02:17:12 | 661 | |||||||||||
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xFITOM Resource Report Resource Website 1+ mentions |
xFITOM (RRID:SCR_014445) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two. | transcription factor, binding site, information theory, customizable program, sequence analysis software |
uses: GenBank is related to: CollecTF |
PMID:21346861 | Available for download, Acknowledgement requested | http://www.mybiosoftware.com/fitom-1-0-detection-binding-sites-dna-rna-sequences.html | compbio.umbc.edu/Software/xFITOM/ http://research.umbc.edu/~erill/ | SCR_014445 | SciCrunch Registry | 2026-09-26 02:17:12 | 7 | |||||||
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NIAID Overview of Coronaviruses Resource Report Resource Website 1+ mentions |
NIAID Overview of Coronaviruses (RRID:SCR_018290) | data or information resource, funding resource, portal, topical portal | Information about coronaviruses, including COVID-19. NIAID provides research funding and resources for scientific community to facilitate development of vaccines, therapeutics, and diagnostics for infectious diseases, including those caused by coronaviruses. | Coronavirus, COVID-19, data, infectious disease, NIAID |
is listed by: Data and Computational Resources to Address COVID-19 is related to: NIAID |
COVID-19 | NIAID | Free, Freely available | SCR_018290 | SciCrunch Registry | 2026-09-26 02:17:16 | 4 | ||||||||
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LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | SciCrunch Registry | 2026-09-26 02:17:15 | 32 | ||||||||
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HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | data processing software, software application, software resource, workflow software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
ABS4NGS project ; ERC Advanced Investigator award ; European Commission ; European Research Coucil ; France Genomique National infrastructure ; Howard Hughes Medical Institute ; Labex Deep ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | SciCrunch Registry | 2026-09-26 02:17:15 | 238 | ||||||
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Thunder Resource Report Resource Website 10+ mentions |
Thunder (RRID:SCR_016556) | data analysis software, data processing software, image analysis software, software application, software resource | Software package for the analysis of image and time series data in Python. Provides data structures and algorithms for loading, processing, and analyzing these data. Runs locally or against a Spark cluster with an identical API. | Free, Available for download, Freely available, Tutorial available | https://github.com/thunder-project/thunder | SCR_016556 | SciCrunch Registry | 2026-09-26 02:17:14 | 10 | |||||||||||
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emmeans Resource Report Resource Website 100+ mentions |
emmeans (RRID:SCR_018734) | data analysis software, data analytics software, data processing software, software application, software resource | Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. | Estimated marginal mean, liner model, mixed model, obtain estimated marginal mean, EMMs, linear function, slope comparison, plot | is related to: CRAN | Free, Available for download, Freely available | https://github.com/rvlenth/emmeans | SCR_018734 | SciCrunch Registry | Least Squares Means, Estimated Marginal Means | 2026-09-26 02:17:18 | 195 |
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