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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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iBioSeminars Resource Report Resource Website |
iBioSeminars (RRID:SCR_005848) | iBioSeminars | data or information resource, training material, video resource, narrative resource | iBioSeminars offers: * Free, on-demand lectures: Many universities/colleges have limited access to high profile leaders in biological research. Our goal is to add 15-20 seminars per year, of similar quality to outstanding lectures that are currently in this library. Access, through web streaming or download, is completely free-of-charge. * Targeting a broad audience: iBioSeminars start with an extended introduction, making them accessible to non-specialists and students, and then progress to cover current research. Senior scientists and students can view and enjoy these lectures. * Education: iBioSeminars are being used by undergraduate and graduate teachers to augment their classroom material. We have now added an education component to this web site (including lecture notes, questions/answers and short video clips for teaching). * International communication: iBioSeminars have viewers in 115 countries and they are being internally promoted in several countries as an educational tool and scientific resource. * Goodwill: Lecturers generously donate their time to prepare these lectures. The project, largely funded by HHMI, is a grass roots efforts with time invested by several individuals at UCSF, HHMI and ASCB. | biological research, biology, lecture, seminar, education, undergraduate, graduate |
has parent organization: University of California at San Francisco; California; USA has parent organization: American Society for Cell Biology has parent organization: Howard Hughes Medical Institute |
NSF ; NIGMS ; Howard Hughes Medical Institute |
Licensed under a Creative Commons Attribution-NonCommercial-NoDerivs v3 Unported License. | nlx_149380 | SCR_005848 | iBioSeminars - Bringing the World''s Best Biology to You, iBioSeminars - Bringing the Worlds Best Biology to You, iBioSeminars.org | 2026-08-10 09:32:40 | 0 | ||||||
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KZNF Catalog Resource Report Resource Website |
KZNF Catalog (RRID:SCR_015495) | data or information resource, database, catalog | Searchable, manually curated collection of Kruppel-type zinc finger genes (KZNFs) in primates with finished or high quality draft genomes. | kruppel type zinc finger gene, kznf, kruppel type zinc finger model, primate finger, primate finger gene | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | Open source | SCR_015495 | 2026-08-10 09:35:31 | 0 | ||||||||||
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Functional Network Connectivity (FNC) Resource Report Resource Website 10+ mentions |
Functional Network Connectivity (FNC) (RRID:SCR_015731) | FNC | data analysis software, software application, software toolkit, software resource, data processing software | Software toolbox which finds and displays temporal relations amongst components. This can help determine causal relations in the brain. | fmri, temporal relation, causal relation, neural connectivity, | is used by: MATLAB | PMID:18082428 | Free, Available for download, Tutorial available | http://mialab.mrn.org/software/fnc/index.html | SCR_015731 | FNC Toolbox, GIFT toolbox, Functional Network Connectivity Toolbox | 2026-08-10 09:35:26 | 26 | ||||||
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LabeledIn Resource Report Resource Website 1+ mentions |
LabeledIn (RRID:SCR_015667) | data or information resource, database, software resource | Database of annotations of drug indications in FDA drug labels. LabeledIn contains an expert curated set of indications and a crowdsourced set of indications. | drug, annotation, fda, fda drug label | Intramural Research Program of the NIH – National Library of Medicine ; National Key Technology R&D Program of China 2013BAI06B01; Fundamental Research Funds for the Central Universities 13R0101; MITRE Internal Research and Development Program |
PMID:25220766 PMID:25797061 |
Public, Freely available, Free, Available for download | SCR_015667 | 2026-08-10 09:35:32 | 2 | |||||||||
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DISEASES Resource Report Resource Website 500+ mentions |
DISEASES (RRID:SCR_015664) | data or information resource, database | Database that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. It also assigns confidence scores that facilitate comparison of the different types and sources of evidence. | disease, gene, disease-gene association, text-mining, , bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation Center for Protein Research NNF14CC0001; European Union Seventh Framework Programme n259348 |
PMID:25484339 | biotools:diseases | https://bio.tools/diseases | SCR_015664 | 2026-08-10 09:35:32 | 655 | |||||||
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TISSUES Resource Report Resource Website 10+ mentions |
TISSUES (RRID:SCR_015665) | data or information resource, web application, database, software resource | Database that integrates evidence on tissue expression from manually curated literature, proteomics and transcriptomics screens, and automatic text mining. It maps all evidence to common protein identifiers and Brenda Tissue Ontology terms, and further unifies it by assigning confidence scores that facilitate comparison of the different types and sources of evidence. | tissue expression, proteomic, transcriptomic, text-mining, brenda tissue ontology, protein identifier, bio.tools |
uses: BRENDA Tissue and Enzyme Source Ontology is listed by: Debian is listed by: bio.tools |
Novo Nordisk Foundation NNF14CC0001; NCI U54 CA189205-01; CSIRO’s OCE Science Leader program |
PMID:26157623 | Freely available, Free, Available for download | biotools:tissues | https://bio.tools/tissues | SCR_015665 | TISSUES: Tissue Expression Database, Tissue Expression Database | 2026-08-10 09:35:25 | 45 | |||||
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Evolutionary Rate Covariation Resource Report Resource Website 1+ mentions |
Evolutionary Rate Covariation (RRID:SCR_015669) | ERC | data analysis software, software application, web application, software resource, data processing software | Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes. | statistical software, correlation, phylogeny, gene extraction, genetic evolutionary history, covariation, group analysis | PMID:25679399 PMID:24453993 PMID:22287101 |
Freely available, Free, Available for download | SCR_015669 | ERC: Evolutionary Rate Covariation, Evolutionary Rate Covariation (ERC) Analysis, Evolutionary Rate Covariation (ERC) | 2026-08-10 09:35:25 | 2 | ||||||||
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Connectivity Map 02 Resource Report Resource Website 100+ mentions |
Connectivity Map 02 (RRID:SCR_015674) | cmap | data or information resource, web application, database, software resource | Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription, expression, gene, drug, disease pattern-matching algorithm, FASEB list |
has parent organization: Broad Institute has parent organization: Broad Institute of MIT and Harvard |
PMID:17008526 | THIS RESOURCE IS NO LONGER IN SERVICE | https://www.broadinstitute.org/cmap_build01 | SCR_015674 | Broad Institute Connectivity Map 02 Build, cmap | 2026-08-10 09:35:25 | 243 | ||||||
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NAPR: Neuroanatomical Age Prediction using R Resource Report Resource Website 1+ mentions |
NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) | NAPR | service resource, storage service resource, data repository | Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3. | neuroanatomy, prediction, r, neuroimaging, mri scan, cortical thickness, relevance vector | DOI:10.1101/099309 | Free, Available for download | http://www.cloudneuro.org/ | SCR_015759 | Neuroanatomical Age Prediction using R | 2026-08-10 09:35:27 | 1 | |||||||
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Decision Decoding Toolbox Resource Report Resource Website 1+ mentions |
Decision Decoding Toolbox (RRID:SCR_015978) | DDTBOX | data analysis software, software application, software toolkit, software resource, data processing software | Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB. | erp, event, related, potential, multivariate, analysis, pattern, matlab, mvpa | Free, Available for download | SCR_015978 | The Decision Decoding Toolbox (DDTBOX), DDTBOX: Decision Decoding Toolbox | 2026-08-10 09:35:35 | 3 | |||||||||
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Brain-CODE Resource Report Resource Website 10+ mentions |
Brain-CODE (RRID:SCR_015877) | service resource, storage service resource, data repository | Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders. | informatics, data storage, brain disorder | brain disorder, neurological disorder, informatics platform, data repository, data storage service, neuroscience | Public, Freely available, The research community can contribute to this resource | r3d100012181 | https://doi.org/10.17616/R3CK9G | SCR_015877 | 2026-08-10 09:35:28 | 49 | ||||||||
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PDB-Dev Resource Report Resource Website 10+ mentions |
PDB-Dev (RRID:SCR_016185) | service resource, storage service resource, data repository | Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations. | protein, prototype, deposition, integration, hybrid, model, macromolecule, assembly, crystallography, spectroscopy, microscopy, |
is related to: IHM-dictionary has parent organization: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA |
NSF DBI-1519158 | Account required, Freely available, The research community can contribute to this resource | SCR_016185 | 2026-08-10 09:35:33 | 36 | |||||||||
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RELION Resource Report Resource Website 100+ mentions |
RELION (RRID:SCR_016274) | data analysis software, software application, standalone software, software resource, data processing software | Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy. | cryo, cryogenic, cryo em, determination, analysis, bayesian, statistic, map, maximum a posteriori, electron, cryomicroscopy |
is listed by: Debian is listed by: OMICtools |
UK Medical Research Council | PMID:23000701 | Free, Available for download, Tutorial available | OMICS_15597 | https://sources.debian.org/src/relion-bin+mpi+gui/ | SCR_016274 | RELION, REgularised LIkelihood OptimisatioN, RELION-3 | 2026-08-10 09:35:37 | 440 | |||||
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ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | data analysis software, software application, software toolkit, standalone software, software resource, data processing software | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-08-10 09:35:36 | 10 | ||||||||||
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MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data analysis software, software application, software toolkit, software resource, data processing software | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-08-10 09:35:37 | 5 | |||||||
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PhenoSpD Resource Report Resource Website 1+ mentions |
PhenoSpD (RRID:SCR_016359) | PSD | data analysis software, software application, software toolkit, software resource, data processing software | Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool. | spectral, decomposition, matrice, phenotypic, correlation, estimation, multiple, testing, correction, human, phenome, genome, summary, statistic, decomposition, matrice, genomics |
is related to: University of Bristol; Bristol; United Kingdom is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016359 | Pheno Spectral Decomposition, PhenoSpD | 2026-08-10 09:35:39 | 6 | ||||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, software application, software toolkit, software resource, data processing software | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-08-10 09:35:36 | 2 | |||||
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migec Resource Report Resource Website 10+ mentions |
migec (RRID:SCR_016337) | MIGEC | data analysis software, software application, software toolkit, software resource, data processing software | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President ; European Regional Development Fund |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-08-10 09:35:38 | 11 | |||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | data analysis software, software application, software toolkit, software resource, data processing software | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-08-10 09:35:39 | 1 | ||||||
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iMITS Resource Report Resource Website |
iMITS (RRID:SCR_016552) | iMITS | data or information resource, database, catalog | This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products. | international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPC |
is affiliated with: International Mouse Phenotyping Consortium (IMPC) is related to: GenTaR |
NIH KOMP2; European Union 223592 |
Restricted | SCR_016552 | international Micro Injection Tracking System | 2026-08-10 09:35:40 | 0 |
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