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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SvABA Resource Report Resource Website 10+ mentions |
SvABA (RRID:SCR_022998) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements. | genome wide detection, structural variants, indels, local assembly | NHGRI T32 HG002295; NCI U54CA143798; NCI R01CA188228; DFCI-Novartis Drug Discovery Program ; Voices Against Brain Cancer ; Pediatric Low-Grade Astrocytoma Foundation ; Broad Institute ; Wellcome Fund Career Award for Medical Scientists |
PMID:29535149 | Free, Available for download, Freely available | SCR_022998 | 2026-08-13 09:30:56 | 18 | |||||||||
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Sirenia Sleep Pro Resource Report Resource Website 1+ mentions |
Sirenia Sleep Pro (RRID:SCR_022918) | data analysis software, data processing software, software resource, software application | Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported. | Pinnacle Technology Inc., data analysis, semi-automated scoring methods, reduce scoring time, sleep data, EEG/EMG data, video data sets | Restricted | SCR_022918 | Pinnacle Sirenia Sleep Pro | 2026-08-13 09:30:40 | 3 | ||||||||||
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CNS Genoscope Resource Report Resource Website 10+ mentions |
CNS Genoscope (RRID:SCR_023020) | data access protocol, software resource, web service | Web tool as Brassica napus genome browser. | Brassica napus, genome browser, Brassica napus genome browser | Free, Freely available | SCR_023020 | 2026-08-13 09:31:00 | 23 | |||||||||||
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YaHS Resource Report Resource Website 500+ mentions |
YaHS (RRID:SCR_022965) | data analysis software, data processing software, software resource, software application | Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies. | construction of chromosome scale scaffolds, Hi-C data, Omni-C data, scaffold contig level assemblies, chromosome scale scaffolded assemblies | Wellcome Trust | DOI:10.1101/2022.06.09.495093 | Free, Available for download, Freely available | SCR_022965 | 2026-08-13 09:30:59 | 806 | |||||||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | ontology, data or information resource, controlled vocabulary | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/, http://bioportal.bioontology.org/ontologies/ECO | SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-08-13 09:26:37 | 19 | |||||
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Medical image simulation Resource Report Resource Website 1+ mentions |
Medical image simulation (RRID:SCR_010355) | OntoVIP | ontology, data or information resource, controlled vocabulary | Ontology that describes the content of the models used in medical image simulation developed in the context of the Virtual Imaging Platform project (VIP), a french project aiming at sharing medical image simulation resources. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI. | owl | is listed by: BioPortal | French National Research Agency ANR-09-COSI-03 | nlx_157472 | SCR_010355 | 2026-08-13 09:28:14 | 3 | ||||||||
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Mental State Assessment Resource Report Resource Website 1+ mentions |
Mental State Assessment (RRID:SCR_010357) | ONL-MSA | ontology, data or information resource, controlled vocabulary | Ontology that is a module of the OntoNeuroLOG ontology that covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Grober-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT). | owl neuroimaging, mri, mental state assessment | is listed by: BioPortal | French National Research Agency ANR-06-TLOG-024 | nlx_157474 | SCR_010357 | MSA ontology | 2026-08-13 09:28:31 | 1 | |||||||
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Abbiotec Resource Report Resource Website 10+ mentions |
Abbiotec (RRID:SCR_013596) | antibody supplier, commercial organization, material resource, reagent supplier | An Antibody supplier | nlx_152243 | SCR_013596 | Abbiotec LLC | 2026-08-13 09:29:05 | 25 | |||||||||||
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IOX2 Resource Report Resource Website 1+ mentions |
IOX2 (RRID:SCR_022973) | data processing software, data acquisition software, software application, analysis service resource, production service resource, service resource, data analysis service, software resource | Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing. | emka TECHNOLOGIES, physiological data, preclinical experiment, real time signal processing, | Restricted | SCR_022973 | 2026-08-13 09:30:40 | 6 | |||||||||||
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Human Tumor Atlas Network Resource Report Resource Website 10+ mentions |
Human Tumor Atlas Network (RRID:SCR_023364) | HTAN | topical portal, data or information resource, disease-related portal, atlas, portal | 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. | Three dimensional atlases, cancer transitions, diverse set of tumor types, map healthy organs, cancer genomics approaches, bulk sequencing at single point in time, data, precancerous lesions to advanced disease, | cancer | National Cancer Institut Cancer Moonshot Initiative | PMID:32302568 | Free, Freely available | SCR_023364 | 2026-08-13 09:30:44 | 42 | |||||||
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FAIR Data Station Resource Report Resource Website 1+ mentions |
FAIR Data Station (RRID:SCR_023239) | FAIR-DS | web application, data or information resource, project portal, software resource, portal | Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start. | FAIR, FAIR data, metadata quality improvement, record meta-data, minimum information standards, FAIR scientific data management, | Dutch national funding agency NWO 184.035.007 | Free, Freely available | http://data.m-unlock.nl, http://fairbydesign.nl, http://gitlab.com/m-unlock/fairds | SCR_023239 | 2026-08-13 09:31:00 | 1 | ||||||||
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Natural Scenes Dataset Resource Report Resource Website 10+ mentions |
Natural Scenes Dataset (RRID:SCR_023648) | NSD | topical portal, data or information resource, data set, portal | Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry. | Natural scenes, vision, fMRI measurements, fMRI dataset, whole brain, healthy adult subjects, images, visual representation and cognition, benchmark, training data | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | PMID:34916659 | Free,Freely available | https://github.com/cvnlab/nsdcode/ | SCR_023648 | 2026-08-13 09:30:48 | 44 | |||||||
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SlideBook Resource Report Resource Website 500+ mentions |
SlideBook (RRID:SCR_014423) | data analysis software, data processing software, software resource, software application | Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton. | SCR_014423 | 2026-08-13 09:29:03 | 986 | |||||||||||||
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loadGffToGe_db for custom genome Resource Report Resource Website 1+ mentions |
loadGffToGe_db for custom genome (RRID:SCR_015997) | data processing software, software resource, data visualization software, software application | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE. | Next Generation Sequencers, Next Generation Sequencers data, Next Generation Sequencers data analysis and visualization, | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | https://cell-innovation.nig.ac.jp/maser/index_en.html | SCR_015997 | Management and Analysis System for Enormous Reads: loadGffToGe_db for custom genome | 2026-08-13 09:29:32 | 1 | ||||||||
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vhlab-TwoPhoton-matlab Resource Report Resource Website 1+ mentions |
vhlab-TwoPhoton-matlab (RRID:SCR_023369) | data analysis software, data processing software, software resource, software application | Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab. | Matlab, calcium imaging data analysis, calcium imaging, images, time series data extraction, | PMID:18946471 | Free, Available for download, Freely available | SCR_023369 | Van Hooser lab fluorescent time-series analysis software | 2026-08-13 09:30:44 | 2 | |||||||||
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MetGENE Resource Report Resource Website 1+ mentions |
MetGENE (RRID:SCR_023402) | data access protocol, software resource, web service | Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype. | Gene centric metabolomics information retrieval, genes and metabolites associations identification, gene centric data aggregator, | has parent organization: University of California at San Diego; California; USA | NIH Common Funds | Free, Freely available | https://bdcw.org/MW/docs/MetGENETutorial.pdf | SCR_023402 | 2026-08-13 09:31:04 | 1 | ||||||||
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partec flomax Resource Report Resource Website 1+ mentions |
partec flomax (RRID:SCR_014026) | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Partec uses FloMax software on most cytometers, which produces FCS 3.0 compliant files. FloMax rescales the fluorescent data on the acquisition display without changing the stored values. | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014026 | 2026-08-13 09:29:07 | 7 | ||||||||||||
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HetMatPy Resource Report Resource Website 1+ mentions |
HetMatPy (RRID:SCR_023409) | data analysis software, data processing software, software application, network analysis software, software resource | Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes. | Hetionet, matrix storage, operations on hetnets, hetnets, heterogeneous networks, | Gordon and Betty Moore Foundation ; NHGRI R01 HG010067; NCI R01 CA237170 |
PMID:36711546 | Free, Available for download, Freely available | SCR_023409 | hetmatpy | 2026-08-13 09:31:03 | 1 | ||||||||
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University of Chicago Digestive Diseases Research Core Center Resource Report Resource Website 1+ mentions |
University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) | DDRCC | data or information resource, organization portal, training resource, portal | Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis. | DDRCC, digestive disease, uchicago |
is listed by: NIDDK Information Network (dkNET) is parent organization of: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Administrative Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core is parent organization of: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core has organization facet: University of Chicago Digestive Diseases Research Core Center Administrative Core has organization facet: University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core has organization facet: University of Chicago Digestive Diseases Research Core Center Tissue Engineering and Cell Models Core has organization facet: University of Chicago Digestive Diseases Research Core Center Host-Microbe Core has organization facet: University of Chicago Digestive Diseases Research Core Center Tissue and Cell Imaging Core is organization facet of: Digestive Disease Centers |
digestive disease | NIDDK P30 DK042086 | Available to the research community | SCR_015601 | 2026-08-13 09:29:24 | 1 | |||||||
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pillow Resource Report Resource Website 10+ mentions |
pillow (RRID:SCR_023337) | software toolkit, software resource, software library | Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool. | Python Imaging Library, image processing capabilities, foundation for general image processing, | Free, Available for download, Freely available | SCR_023337 | 2026-08-13 09:31:02 | 13 |
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