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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Clearcut Resource Report Resource Website 10+ mentions |
Clearcut (RRID:SCR_016059) | data processing software, data visualization software, software application, software resource, standalone software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023.Software as a stand-alone reference implementation for the Relaxed Neighbor Joining (RNJ) algorithm. Used in distance-based phylogenetic tree reconstruction method to process large sequence datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rnj, phylogenetic, tree, construction, neighbor, joining, distance, method, reference, standalone, implemetation, relaxed, algorithm, phylogenetic, tree, reconstruction, sequence |
is listed by: Debian is listed by: OMICtools is related to: University of Idaho; Idaho; USA |
INBRE Program of the National Center for Research Resources ; NIH P20 RR16448; NIH P20 RR16454; NSF EPS 00809035 |
PMID:16752216 DOI:10.1007/s00239-005-0176-2 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15083 | https://github.com/ibest/clearcut, https://sources.debian.org/src/clearcut/ | SCR_016059 | 2026-09-12 12:58:34 | 26 | ||||||
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NHGRI U54 HG008097; NIGMS R01 GM103551; NIGMS R01 GM121696; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-09-12 12:58:49 | 0 | ||||||
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NIH Figshare Archive Resource Report Resource Website 1+ mentions |
NIH Figshare Archive (RRID:SCR_017580) | NIH Figshare | data or information resource, data repository, database, service resource, storage service resource | Repository to make datasets resulting from NIH funded research more accessible, citable, shareable, and discoverable. Data submitted will be reviewed to ensure there is no personally identifiable information in data and metadata prior to being published and in line with FAIR -Findable, Accessible, Interoperable, and Reusable principles. Data published on Figshare is assigned persistent, citable DOI (Digital Object Identifier) and is discoverable in Google, Google Scholar, Google Dataset Search, and more.Complited on July,2020. Researches can continue to share NIH funded data and other research product on figshare.com. | Respository, data, NIH funded, data set, FAIR |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: FigShare is related to: FigsharePlus |
NIH | Restricted | SCR_017580 | NIH, Figshare, Fig Share, NIH Figshare, NIH Fig share, National Institute of Health | 2026-09-12 12:58:54 | 9 | |||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, data or information resource, database, production service resource, service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
Department of Health and Human Services ; NIDA ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-09-12 12:58:54 | 8 | ||||||
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Distributed Archives for Neurophysiology Data Integration Resource Report Resource Website 50+ mentions |
Distributed Archives for Neurophysiology Data Integration (RRID:SCR_017571) | DANDI | data repository, service resource, storage service resource | Free, cloud-based platform for publishing, sharing, and processing standardized neurophysiology data, primarily using the Neurodata Without Borders (NWB) format. Supported by the BRAIN Initiative, it enables researchers to collaborate, reuse datasets, and adhere to FAIR data principles. | publishing data, sharing data, processing data, neurophysiology data, BRAIN Initiative, |
is used by: BICCN is recommended by: BRAIN Initiative is listed by: DataCite is listed by: FAIRsharing is related to: BRAIN Initiative is related to: Allen Institute for Brain Science is related to: NeuroSift is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research |
NIH R24 MH117295 | Free, Freely available | DOI:10.25504/FAIRsharing.f2c119, DOI:10.48324, r3d100013638 | https://doi.org/10.48324/, https://dx.doi.org/10.48324/, https://fairsharing.org/10.25504/FAIRsharing.f2c119, https://doi.org/10.17616/R31NJN0M | SCR_017571 | 2026-09-12 12:58:54 | 58 | ||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | Alfred P. Sloan Foundation Research Fellowship ; NIH DP2 HD088158 |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-09-12 12:58:38 | 227 | ||||||||
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MAST Resource Report Resource Website 100+ mentions |
MAST (RRID:SCR_016340) | MAST | data analysis software, data processing software, software application, software resource, software toolkit | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | Bill and Melinda Gates Foundation OPP1032317; NIBIB R01 EB008400; NIH DP2 DE023321 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-09-12 12:58:38 | 106 | ||||||
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MAxEntScan Resource Report Resource Website 50+ mentions |
MAxEntScan (RRID:SCR_016707) | MAxEntScan | service resource, simulation software, software application, software resource | Software tool as a framework for modeling the sequences of short sequence motifs based on the maximum entropy principle (MEP). Used for sequence motifs such as those involved in RNA splicing. | modeling, sequence, short, motif, maximum, entropy, principle, MEP, RNA, splicing |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Lee Kuan Yew Scholarship for the goverment of Singapore ; NIH ; NSF Grant 0218506 |
PMID:15285897 | Free, Available for download, Freely available | SCR_016707 | Maximum Entropy Scan, MAxEntScan, MAximumEntropyScan | 2026-09-12 12:58:43 | 70 | ||||||
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NIAID Resource Report Resource Website 500+ mentions |
NIAID (RRID:SCR_016598) | NIAID | data or information resource, disease-related portal, organization portal, portal, topical portal | National Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases. | immunologic, allergic, infectious, disease, institute, treat, prevent |
lists: Nephele lists: PaVE lists: ChemokineDB lists: SPICE lists: TRIAGE lists: NGlycPred lists: dCAS lists: HASP lists: ABC Bacterial Transporter Systems Database lists: TB PORTALS lists: JOINSOLVER is related to: The Immunology Database and Analysis Portal (ImmPort) is related to: The 10000 Immunomes is related to: NIAID Overview of Coronaviruses is parent organization of: OMiCC is parent organization of: OCICB is parent organization of: NetCirChro is parent organization of: Immune Epitope Database and Analysis Resource (IEDB) |
NIH | SCR_016598 | National Institute of Allergy and Infectious Diseases | 2026-09-12 12:58:42 | 575 | ||||||||
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SPICE Resource Report Resource Website 50+ mentions |
SPICE (RRID:SCR_016603) | SPICE | data analysis software, data processing software, data visualization software, software application, software resource | Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically. | data, mining, visualization, analysis, polychromatic, flow, cytometry, dataset, normalized, graphically, bio.tools |
is listed by: NIAID is listed by: Debian is listed by: bio.tools |
NIAID ; NIH |
PMID:21265010 | Free, Available for download, Freely available | biotools:spice | https://bio.tools/spice | SCR_016603 | Simplified Presentation of Incredibly Complex Evaluations | 2026-09-12 12:58:42 | 72 | ||||
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Cleveland Family Study Resource Report Resource Website 1+ mentions |
Cleveland Family Study (RRID:SCR_016585) | CFS | data or information resource, disease-related portal, portal, topical portal | Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore. | data, polysomnography, sleep apnea, family, familial aggregation, EEG, ECG, longitudinal | is listed by: National Sleep Research Resource (NSRR) | sleep disorder | NCRR M01 RR00080; NHLBI HL46380; NHLBI T32 HL07567; NIH R01 46380 |
PMID:7881656 | SCR_016585 | Cleveland Family Study | 2026-09-12 12:58:41 | 4 | ||||||
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CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data analysis software, data processing software, image analysis software, software application, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-09-12 12:58:45 | 18 | ||||||||
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ValIdated Systematic IntegratiON of epigenomic data Resource Report Resource Website 10+ mentions |
ValIdated Systematic IntegratiON of epigenomic data (RRID:SCR_016921) | VISION | catalog, data or information resource, database, portal, project portal | International project to analyze mouse and human hematopoiesis, and provide a tractable system with clear clinical significance and importance to NIDDK. Collection of information from the flood of epigenomic data on hematopoietic cells as catalogs of validated regulatory modules, quantitative models for gene regulation, and a guide for translation of research insights from mouse to human. | analyze, mouse, human, hematopoietic, cell, blood, component, collection, epigenomic, data, catalog, gene, regulation | is listed by: NIDDK Information Network (dkNET) | National Institute for Diabetes and Digestive Diseases ; NIDDK ; NIH |
SCR_016921 | ValIdated Systematic IntegratiON of epigenomic data, ValIdated Systematic IntegratiON | 2026-09-12 12:58:45 | 11 | ||||||||
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Knockout Mouse Project Resource Report Resource Website 10+ mentions |
Knockout Mouse Project (RRID:SCR_005571) | KOMP, NIH KOMP | data or information resource, portal, project portal | Project is providing critical tools for understanding gene function and genetic causes of human diseases. Project KOMP is focused on generating targeted knockout mutations in mouse ES cells. Second phase, KOMP2, relies upon successful generation of strains of knockout mice from these ES cells. Information from JAX about their contributions to KOMP project. | Generating, knockout, mutation, mouse, ES cell, embryonic, stem, c57bl/6 |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: KOMP2 is related to: KOMP2 is related to: StatPackets has parent organization: International Knockout Mouse Consortium has parent organization: National Institutes of Health is parent organization of: Knockout Mouse Project Repository is parent organization of: Knockout Mouse Project Repository at JAX |
NIH Blueprint for Neuroscience Research ; NIH |
Free, Freely available | SCR_017527, nlx_145296 | https://grants.nih.gov/grants/guide/rfa-files/rfa-rr-06-005.html | http://www.nih.gov/science/models/mouse/knockout/index.html | SCR_005571 | NIH Knockout Mouse Project, Knock-Out Mouse Project | 2026-09-12 01:00:56 | 10 | ||||
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NIH Clinical Collection Resource Report Resource Website 10+ mentions |
NIH Clinical Collection (RRID:SCR_007349) | NCC | material resource, reagent supplier | A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas. | clinical, collection, drug, compound, chemistry, medicinal chemistry, target, affinity, human, disease, disorder, small molecule | is related to: Molecular Libraries Program | NIH | nif-0000-00254 | SCR_007349 | 2026-09-12 01:00:57 | 14 | ||||||||
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Human Microbiome Project Resource Report Resource Website 100+ mentions |
Human Microbiome Project (RRID:SCR_012956) | HMP, NIH HMP, HMP1 | data or information resource, portal, project portal | NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016. | generate, resource, human, body, microbiota, analyze, health, disease, metagenomic, DNA, sequesncing, data |
lists: Pathogen Portal lists: DNACLUST lists: QIIME lists: mothur lists: Greengenes lists: Ribosomal Database Project lists: DeconSeq lists: FragGeneScan lists: MetAMOS lists: MetaPhlAn lists: MetaPhyler lists: METAREP lists: PRINSEQ lists: TagCleaner lists: BioCyc lists: MG-RAST lists: Core Gene Evaluation Script lists: IMG System lists: RAST Server lists: GINGKO lists: inVUE lists: LEfSe lists: Metastats lists: MicrobiomeUtilities lists: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP lists: HMPTrees lists: Simrank lists: speciateIT lists: Unifrac lists: Fast-Unifrac lists: SitePainter lists: BMTagger lists: HUMAnN lists: Metapath lists: IMG System is related to: biobakery is related to: Integrative Human Microbiome Project is related to: MicrobiomeDB is related to: Broad Institute Genomics Platform has parent organization: National Institutes of Health is parent organization of: HMP Data Analysis and Coordination Center |
NIH | nif-0000-25316 | https://www.hmpdacc.org/ihmp/, https://www.hmpdacc.org/hmp | http://nihroadmap.nih.gov/hmp/ | SCR_012956 | Human Microbiome Project, NIH HMP, HMP1, HMP, NIH Human Microbiome Project | 2026-09-12 01:01:01 | 414 | |||||
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FuncAssociate: The Gene Set Functionator Resource Report Resource Website 10+ mentions |
FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) | FuncAssociate | analysis service resource, data analysis service, production service resource, service resource | A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool | gene, gene ontology, statistical analysis, web service, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology has parent organization: Roth Laboratory |
NIH ; Canadian Institute for Advanced Research ; NINDS NS054052; NINDS NS035611; NHLBI HL081341; NHGRI HG0017115; NHGRI HG004233; NHGRI HG003224 |
PMID:19717575 PMID:14668247 |
Free for academic use, Acknowledgement requested | biotools:funcassociate, OMICS_02264, nlx_149233 | http://llama.mshri.on.ca/cgi/func/funcassociate, https://bio.tools/funcassociate | SCR_005768 | 2026-09-12 01:01:39 | 36 | |||||
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BARD Resource Report Resource Website 100+ mentions |
BARD (RRID:SCR_006283) | BARD | data or information resource, database | Database that allows scientists without specialized training to effectively utilize Molecular Libraries Program (MLP) data. It allows the research community to utilize and develop new chemical probes to explore biological functions by building a central, permanently accessible link to all aspects of chemical biology data and analyses. The project is split into two basic segments, the first segment delivering functionality for a data dictionary, as well as assay protocol and data entry tools. The second builds a data warehouse for analysis and visualization, accessible through a public RESTful API. They will initially deploy two clients that will use this API - a web-based interface and a desktop application. Advanced access to data and the platforms will also be available to support plug-in development and the repackaging of data by others. Initially the project will focus on small molecule assays. Features: * allow scientists to annotate assay data using a common, shared language * provide facile access to data, integrating existing chemical biology and computational resources * enable meaningful analysis and interpretation of discovery data by the research community * support hypothesis generation for iterative probe- and drug-discovery projects * inform the entire small molecule discovery and development process, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chemical biology, chemical probe, small molecule, drug discovery, data set, FASEB list |
is listed by: 3DVC is related to: Molecular Libraries Program has parent organization: Broad Institute has parent organization: National Institutes of Health |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151903 | SCR_006283 | BioAssay Research Database, BioAssay Research Database (BARD) | 2026-09-12 01:01:42 | 135 | ||||||
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Yeast Intron Database Resource Report Resource Website 1+ mentions |
Yeast Intron Database (RRID:SCR_007144) | Yeast Intron Database | data or information resource, database | Database of information about the spliceosomal introns of the yeast Saccharomyces cerevisiae. Listed are known spliceosomal introns in the yeast genome and the splice sites actually used are documented. Through the use of microarrays designed to monitor splicing, they are beginning to identify and analyze splice site context in terms of the nature and activities of the trans-acting factors that mediate splice site recognition. In version 3.0, expression data that relates to the efficiency of splicing relative to other processes in strains of yeast lacking nonessential splicing factors is included. These data are displayed on each intron page for browsing and can be downloaded for other types of analysis. | intron, spliceosomal, splicing, genome, intron splice signal, sequence, splice site |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
W. M. Keck Foundation ; Packard Foundation ; NIH |
PMID:11988574 | The community can contribute to this resource | nif-0000-03649, OMICS_01890 | http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | SCR_007144 | Ares lab Yeast Intron Database | 2026-09-12 01:01:46 | 2 | ||||
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CRCView Resource Report Resource Website |
CRCView (RRID:SCR_007092) | CRCView | analysis service resource, data analysis service, production service resource, service resource | Web-based microarray data analysis and visualization system powered by CRC, or Chinese Restaurant cluster, a Dirichlet process model-based clustering algorithm recently developed by Dr. Steve Qin. It also incorporates several gene expression analysis programs from Bioconductor, including GOStats, genefilter, and Heatplus. CRCView also installs from the Bioconductor system 78 annotation libraries of microarray chips for human (31), mouse (24), rat (14), zebrafish (1), chicken (1), Drosophila (3), Arabidopsis (2), Caenorhabditis elegans (1), and Xenopus Laevis (1). CRCView allows flexible input data format, automated model-based CRC clustering analysis, rich graphical illustration, and integrated Gene Ontology (GO)-based gene enrichment for efficient annotation and interpretation of clustering results. CRC has the following features comparing to other clustering tools: 1) able to infer number of clusters, 2) able to cluster genes displaying time-shifted and/or inverted correlations, 3) able to tolerate missing genotype data and 4) provide confidence measure for clusters generated. You need to register for an account in the system to store your data and analyses. The data and results can be visited again anytime you log in. | microarray, gene expression, cluster, gene, expression profile, data repository, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
University of Michigan; Michigan; USA ; Institutional Fund ; NIH U013422; NIAID 1R21AI057875-01 |
PMID:17485426 | Registration required | biotools:crcview, nlx_99864 | https://bio.tools/crcview | http://helab.bioinformatics.med.umich.edu/crcview/ | SCR_007092 | Chinese Restaurant ClusterView | 2026-09-12 01:01:45 | 0 |
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