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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SpaSNE Resource Report Resource Website 1+ mentions |
SpaSNE (RRID:SCR_026223) | software application, source code, software resource | Software extension of t-distributed stochastic neighbor embedding, the spatially resolved t-SNE (SpaSNE) designed to preserve both global gene expression and spatial structure for spatially resolved profiling data. Gives comprehensive low-dimensional visualization that could best reflect the molecular similarities of cells and the spatial interactions between cells. | global gene expression, spatial structure, spatially resolved profiling data, low-dimensional visualization, | Free, Available for download, Freely available | SCR_026223 | 2026-08-10 09:38:04 | 1 | |||||||||||
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NIST Chemistry WebBook Resource Report Resource Website 50+ mentions |
NIST Chemistry WebBook (RRID:SCR_026225) | data or information resource, database | Database that provides access to organic compounds data compiled and distributed by NIST under the Standard Reference Data Program. | National Institute of Standards and Technology U.S. Department of Commerce, Standard Reference Data Program, organic compounds data, | Free, Freely available | SCR_026225 | National Institute of Standards and Technology Chemistry WebBook | 2026-08-10 09:38:04 | 76 | ||||||||||
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CancerSEA Resource Report Resource Website 100+ mentions |
CancerSEA (RRID:SCR_026155) | data or information resource, database | Database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. Provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. Provides interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of cancer single cells and corresponding PCGs/lncRNAs expression profiles. | cancer single cells, PCGs/lncRNAs expression profiles, distinct functional states of cancer cells, single-cell level, searching, browsing, visualizing and downloading, functional state activity profiles, | National High Technology Research and Development Program of China ; National Natural Science Foundation of China |
PMID:30329142 | Free, Freely available | SCR_026155 | Cancer Single-cell State Atlas | 2026-08-10 09:38:03 | 202 | ||||||||
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DSigDB Resource Report Resource Website 100+ mentions |
DSigDB (RRID:SCR_026202) | data or information resource, database | Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | , Drug Signatures Database, drug SIGnatures DataBase | 2026-08-10 09:38:04 | 165 | ||||||||
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watvina Resource Report Resource Website 1+ mentions |
watvina (RRID:SCR_026282) | software application, source code, software resource | Software tool as implicit or explicit water model based docking with Autodock vina engine, supporting pharmacophore /position constrained docking.Facilitates drug design with support for explicit or implicit waters, pharmacophore or position-constrained docking, and external torsion parameters (akin to amber/gaff/charmm force fields). Water Model supported protein-ligand docking with Autodock Vina engine. | Water Model, protein-ligand docking, Autodock Vina engine, | Free, Available for download, Freely available, | SCR_026282 | 2026-08-10 09:38:05 | 7 | |||||||||||
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HapHiC Resource Report Resource Website 10+ mentions |
HapHiC (RRID:SCR_026284) | software application, source code, software resource | Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules. | reference-independent, allele-aware scaffolding tool, performance on chromosome assignment, contig ordering and orientation, Hi-C data, scaffold haplotype-phased genome assemblies, chromosome-scale pseudomolecules, | National Natural Science Foundation of China | PMID:39103456 | Free, Available for download, Freely available | SCR_026284 | 2026-08-10 09:38:05 | 27 | |||||||||
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SeuratExtend Resource Report Resource Website 1+ mentions |
SeuratExtend (RRID:SCR_026143) | data analysis software, software application, software toolkit, software resource, data processing software | Software R package that streamlines single-cell RNA-seq analysis by integrating essential tools and databases with the Seurat framework. Provides comprehensive functionality for functional enrichment, trajectory inference, gene regulatory network reconstruction, and enhanced visualization. | single-cell RNA-seq analysis, functional enrichment, trajectory inference, gene regulatory network reconstruction, enhanced visualization, | DOI:10.1101/2024.08.01.606144 | Free, Available for download, Freely available | https://huayc09.github.io/SeuratExtend/ | SCR_026143 | 2026-08-10 09:38:03 | 6 | |||||||||
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Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | data analysis software, data processing software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | Parallel META, Parallel Meta | 2026-08-11 09:40:06 | 4 | |||||||
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BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data analysis software, software application, software resource, data processing software, data visualization software | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-08-11 09:40:10 | 1 | |||||
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Orphelia Resource Report Resource Website 1+ mentions |
Orphelia (RRID:SCR_000119) | simulation software, software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment. | metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment | is listed by: OMICtools | PMID:19429689 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01492 | SCR_000119 | 2026-08-11 09:40:06 | 2 | ||||||||
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RefFinder Resource Report Resource Website 10+ mentions |
RefFinder (RRID:SCR_000472) | RefFinder | service resource, analysis service resource, web service, software resource, production service resource, data access protocol | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene expression, reference gene, web based tool |
uses: BestKeeper uses: NormFinder uses: geNORM is listed by: OMICtools has parent organization: East Carolina University; Carolina; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02321 | http://www.leonxie.com/referencegene.php | SCR_000472 | 2026-08-11 09:40:09 | 45 | |||||||
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Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | data or information resource, database, controlled vocabulary, ontology | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/, https://bio.tools/disease_ontology, http://purl.obolibrary.org/obo/doid.obo, | http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-08-11 09:40:09 | 5 | |||
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Gazetteer Resource Report Resource Website 1+ mentions |
Gazetteer (RRID:SCR_000473) | GAZ | portal, topical portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. | obo, owl |
is listed by: BioPortal is listed by: OBO has parent organization: Genomic Standards Consortium |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157412 | http://purl.obolibrary.org/obo/gaz.owl, http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/gaz.obo | http://gensc.org/gc_wiki/index.php/GAZ_Project | SCR_000473 | 2026-08-11 09:40:09 | 1 | ||||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | data or information resource, consortium, portal, organization portal | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | 2026-08-11 09:40:07 | 3 | |||||||
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ECNP Resource Report Resource Website 1+ mentions |
ECNP (RRID:SCR_000501) | ECNP | data or information resource, portal, community building portal | A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity. | brain, neuroscience, disease mechanism, medicine, clinical, disease | is parent organization of: Preclinical Data Forum Network | Brain disorder | nlx_158605 | SCR_000501 | European College of Neuropsychopharmacology, ECNP - neuroscience applied | 2026-08-11 09:40:10 | 1 | |||||||
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National MS Society Resource Report Resource Website 10+ mentions |
National MS Society (RRID:SCR_000104) | National MS Society | portal, topical portal, funding resource, data or information resource, disease-related portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward. | multiple sclerosis, award, grant, postdoctoral fellowship | Multiple Sclerosis | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143693 | SCR_000104 | National Multiple Sclerosis Society | 2026-08-11 09:40:06 | 34 | |||||||
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RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software resource, software application | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-08-11 09:40:07 | 115 | ||||||
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TEDDY Resource Report Resource Website 1+ mentions |
TEDDY (RRID:SCR_000383) | TEDDY | portal, clinical trial, data or information resource, consortium, database, organization portal | International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. | consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization |
is listed by: One Mind Biospecimen Bank Listing is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository is related to: Teddy study IA prediction has parent organization: University of South Florida; Florida; USA |
Type 1 diabetes, Diabetes | NIDDK 2UC4DK063829 | PMID:21564455 | nlx_152857 | SCR_000383 | The Environmental Determinants of Diabetes in the Young, TEDDY study | 2026-08-11 09:40:08 | 3 | |||||
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Local Binary Pattern Analysis Tools for MR Brain Images Resource Report Resource Website 1+ mentions |
Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) | LBP Analysis Tools for MR Brain Images | software application, image analysis software, image processing software, software resource, data processing software | The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology. | free for non-commercial use only, mr | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155652 | SCR_000412 | 2026-08-11 09:40:09 | 1 | ||||||||
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uManager Resource Report Resource Website 100+ mentions |
uManager (RRID:SCR_000415) | software application, software toolkit, data processing software, software resource, data acquisition software | Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. | microscopy, plugin, data acquisition, automated microscope control, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ImageJ has parent organization: University of California at San Francisco; California; USA |
Free, Available for download, Freely available | SCR_016865, nlx_155812 | https://micro-manager.org/wiki/Download_Micro-Manager_Latest_Release, https://sources.debian.org/src/micromanager/, http://www.nitrc.org/projects/micromanager | SCR_000415 | Micro-Manager, Micro Manager | 2026-08-11 09:40:09 | 285 |
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