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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Musculoskeletal Knowledge Portal Resource Report Resource Website 10+ mentions |
Musculoskeletal Knowledge Portal (RRID:SCR_023171) | MSK-KP | data or information resource, topical portal, portal, disease-related portal | Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data. | genomic data mining, human genetic data, genomic information, musculoskeletal traits and diseases data, DRKB | musculoskeletal disease | NIH AR085003 | PMID:34686856 | Free, Freely available | https://msk.hugeamp.org/ | SCR_023171 | 2026-08-11 09:44:30 | 26 | ||||||
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PURPLE Resource Report Resource Website 1+ mentions |
PURPLE (RRID:SCR_022999) | data analysis software, data processing software, software resource, software application | Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity. | WGS data, whole genome sequenced data, purity ploidy estimator | Free, Available for download, Freely available | SCR_022999 | purity ploidy estimator | 2026-08-11 09:44:29 | 8 | ||||||||||
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FreeStyle 1.8 SP1 Resource Report Resource Website 10+ mentions |
FreeStyle 1.8 SP1 (RRID:SCR_022877) | data analysis software, data processing software, software resource, software application | Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system. | Fisher Scientific, liquid chromatography, mass spectrometry, visualize and qualitatively analyze mass spectrometry data | Restricted | SCR_022877 | 2026-08-11 09:44:27 | 10 | |||||||||||
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SvABA Resource Report Resource Website 10+ mentions |
SvABA (RRID:SCR_022998) | data analysis software, software application, software resource, data processing software, 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 | 2026-08-11 09:44:31 | 18 | |||||||||
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loadBAM2ge_db Resource Report Resource Website 1+ mentions |
loadBAM2ge_db (RRID:SCR_015951) | software application, data processing software, software resource, data visualization software | Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer. | bam, map, mapping, genome, pipeline, maser, visualization, explorer | Public | SCR_015951 | loadBAM2ge_db (PE) | 2026-08-11 09:43:10 | 1 | ||||||||||
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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 | 2026-08-11 09:44:22 | 3 | ||||||||||
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CNS Genoscope Resource Report Resource Website 10+ mentions |
CNS Genoscope (RRID:SCR_023020) | web service, software resource, data access protocol | Web tool as Brassica napus genome browser. | Brassica napus, genome browser, Brassica napus genome browser | Free, Freely available | SCR_023020 | 2026-08-11 09:44:23 | 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 | 2026-08-11 09:44:28 | 806 | |||||||||
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NicheNet Resource Report Resource Website 50+ mentions |
NicheNet (RRID:SCR_023158) | software application, simulation software, software resource | Software tool as R implementation of NicheNet method to predict active ligand-target links between interacting cells. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest. | predict ligand-receptor interactions, intercellular communication, predict active ligand target interactions, interacting cells prediction, | Research Foundation—Flanders ; Flemish Government |
PMID:31819264 | Free, Available for download, Freely available | SCR_023158 | 2026-08-11 09:44:24 | 73 | |||||||||
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ModFit LT Resource Report Resource Website 100+ mentions |
ModFit LT (RRID:SCR_016106) | software application, data processing software, software resource, data visualization software | Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software. | flow, cytometry, histogram, model, graph, cell, tracking, dye, cell line | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_016106 | Verity Software House ModFit LT | 2026-08-11 09:43:17 | 154 | |||||||||
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Abbiotec Resource Report Resource Website 10+ mentions |
Abbiotec (RRID:SCR_013596) | antibody supplier, reagent supplier, commercial organization, material resource | An Antibody supplier | nlx_152243 | SCR_013596 | Abbiotec LLC | 2026-08-11 09:42:39 | 25 | |||||||||||
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IOX2 Resource Report Resource Website 1+ mentions |
IOX2 (RRID:SCR_022973) | service resource, software application, analysis service resource, data processing software, software resource, data analysis service, production service resource, data acquisition software | 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 | 2026-08-11 09:44:29 | 6 | |||||||||||
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Human Tumor Atlas Network Resource Report Resource Website 10+ mentions |
Human Tumor Atlas Network (RRID:SCR_023364) | HTAN | portal, topical portal, atlas, data or information resource, disease-related 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 | 2026-08-11 09:44:36 | 42 | |||||||
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FAIR Data Station Resource Report Resource Website 1+ mentions |
FAIR Data Station (RRID:SCR_023239) | FAIR-DS | portal, project portal, web application, data or information resource, software resource | 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 | 2026-08-11 09:44:25 | 1 | ||||||||
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openMINDS SANDS metadata model Resource Report Resource Website 1+ mentions |
openMINDS SANDS metadata model (RRID:SCR_023498) | openMINDS_SANDS, openMINDS SANDS | data or information resource, standard specification, narrative resource | One of the metadata models of openMINDS metadata framework. Composed of modular metadata schemas for spatial anchoring of neuroscience data structures, including brain atlas definitions. | open science, metadata schema, graph metadata model |
is related to: openMINDS metadata framework is related to: openMINDS controlledTerms metadata model |
European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA1 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA2 785907; European Union’s Horizon 2020 Framework Programme for Research and Innovation - Human Brain Project SGA3 945539; Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) ; European Union’s Research and Innovation Program Horizon Europe - EBRAINS 2.0 101147319 |
Free, Available for download, Freely available | https://openminds-documentation.readthedocs.io/en/latest/schema_specifications/SANDS.html | https://github.com/HumanBrainProject/openMINDS_SANDS | SCR_023498 | 2026-08-11 09:44:27 | 3 | ||||||
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Natural Scenes Dataset Resource Report Resource Website 10+ mentions |
Natural Scenes Dataset (RRID:SCR_023648) | NSD | data or information resource, topical portal, portal, data set | 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 | 2026-08-11 09:44:41 | 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 | 2026-08-11 09:42:49 | 986 | |||||||||||||
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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 | 2026-08-11 09:44:36 | 2 | |||||||||
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MetGENE Resource Report Resource Website 1+ mentions |
MetGENE (RRID:SCR_023402) | web service, software resource, data access protocol | 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 | 2026-08-11 09:44:33 | 1 | ||||||||
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partec flomax Resource Report Resource Website 1+ mentions |
partec flomax (RRID:SCR_014026) | portal, topical portal, data or information resource | 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 | 2026-08-11 09:42:43 | 7 |
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