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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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sei Resource Report Resource Website 10+ mentions |
sei (RRID:SCR_022571) | web service, software resource, data access protocol | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-08-11 09:44:20 | 10 | ||||||||
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pMAT Resource Report Resource Website 1+ mentions |
pMAT (RRID:SCR_022570) | pMAT | data analysis software, data processing software, software resource, software application | Open source software suite for analysis of fiber photometry data. | fiber photometry data analysis, fiber photometry | NIDA DA043572 | PMID:33385438 | SCR_022570 | Photometry Modular Analysis Tool | 2026-08-11 09:44:23 | 8 | ||||||||
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Rphenograph Resource Report Resource Website 10+ mentions |
Rphenograph (RRID:SCR_022603) | data analysis software, data processing software, software resource, software application | Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis. | R, high dimensional single cell data analysis, clustering method |
is related to: Phenograph is related to: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_022603 | 2026-08-11 09:44:20 | 29 | ||||||||||
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IBM SPSS Amos Resource Report Resource Website 10+ mentions |
IBM SPSS Amos (RRID:SCR_022686) | data analysis software, data processing software, software resource, software application | Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance. | regression, factor analysis, correlation and analysis of variance | is related to: IBM SPSS Statistics | Restricted | SCR_022686 | SPSS Amos | 2026-08-11 09:44:27 | 10 | |||||||||
|
Enhancing Quality In Preclinical Data Quality System Resource Report Resource Website 1+ mentions |
Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) | data or information resource, standard specification, narrative resource | Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD. | EQIPD certification, guidance on expectations, Enhancing Quality In Preclinical Data, EQIPD consortium, GoEQIPD, reliable preclinical data generation | PMID:34028353 | Free, Freely available | SCR_022729 | EQIPD Quality System | 2026-08-11 09:44:26 | 1 | |||||||||
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Meta Essentials Resource Report Resource Website 10+ mentions |
Meta Essentials (RRID:SCR_022464) | data analysis software, data processing software, software resource, software application | Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more. | meta analysis, relationship between independent and dependent variable analysis | DOI:10.1002/jrsm.1260 | Free, Available for download, Freely available | SCR_022464 | Meta-Essentials | 2026-08-11 09:44:19 | 35 | |||||||||
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Hexamer Additive Linear Resource Report Resource Website 1+ mentions |
Hexamer Additive Linear (RRID:SCR_022581) | HAL | web service, software resource, data access protocol | Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events. | sequence variants on alternative splicing prediction, cassete exon, skipped exon events, changes in alternative 5' splice events, | National Science Foundation Career Award ; Burroughs Wellcome Career Award at the Scientific Interface |
DOI:10.1016/j.cell.2015.09.054 | Free, Freely available | SCR_022581 | 2026-08-11 09:44:25 | 1 | ||||||||
|
NetShift Resource Report Resource Website 10+ mentions |
NetShift (RRID:SCR_022733) | web service, software resource, data access protocol | Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets. | Driver microbes, identification of driver nodes, case control association networks, driver nodes between networks | CSIR-National Chemical Laboratory ; Academy of Scientific and Innovative Research |
PMID:30287886 | Free, Freely available | SCR_022733 | Netshif | 2026-08-11 09:44:28 | 10 | ||||||||
|
UpSet Resource Report Resource Website 10+ mentions |
UpSet (RRID:SCR_022731) | data analysis software, software application, software resource, data processing software, data visualization software | Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets. | visualize set intersections, matrix layout, intersecting sets, more than three sets quantitative data analysis | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | https://github.com/VCG/upset | SCR_022731 | UpSet Plot | 2026-08-11 09:44:21 | 16 | |||||||
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VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | web service, software resource, data access protocol | Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses. | genomic data integration, support systems biology, genomic data visualization and analysis | NSF DBI 0445666; NSF IOB 0519985; NSF MCB–0209754; FONDECYT ; Grape Genomics ; Millennium Nucleus for Plant Functional Genomics ; NIGMS R01 GM 032877; NIGMS 5F32GM75600 |
PMID:20007449 | Free, Available for download, Freely available | SCR_022576 | VirtualPlant 1.3 | 2026-08-11 09:44:23 | 3 | ||||||||
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GASVPro Resource Report Resource Website 1+ mentions |
GASVPro (RRID:SCR_005259) | GASVPro | data analysis software, software application, software resource, data processing software, sequence analysis software | Software tool combining both paired read and read depth signals into probabilistic model which can analyze multiple alignments of reads. Used to find structural variation in both normal and cancer genomes using data from variety of next-generation sequencing platforms. Used to predict structural variants directly from aligned reads in SAM/BAM format.Combines read depth information along with discordant paired read mappings into single probabilistic model two common signals of structural variation. When multiple alignments of read are given, GASVPro utilizes Markov Chain Monte Carlo procedure to sample over the space of possible alignments. | structural variation, genome, genomics, alignment, sequencing, variant, variation, detection, dna, paired, end, read, sequence |
is listed by: OMICtools is related to: GASV has parent organization: Brown University; Rhode Island; USA |
NHGRI R01 HG5690; Burroughs Wellcome Career Award at the Scientific Interface |
PMID:22452995 | Free, Available for download, Freely available | OMICS_00317 | http://code.google.com/p/gasv/downloads/list | SCR_005259 | GASVPro: Geometric Analysis of Structural Variants | 2026-08-11 09:41:16 | 8 | ||||
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HeadIT Resource Report Resource Website 1+ mentions |
HeadIT (RRID:SCR_005657) | HeadIT | service resource, data or information resource, storage service resource, data set, data repository | Platform for sharing, download, and re-analysis or meta-analysis of sophisticated, fully annotated, human electrophysiological data sets. It uses EEG Study Schema (ESS) files to provide task, data collection, and subject metadata, including Hierarchical Event Descriptor (HED) tag descriptions of all identified experimental events. Visospatial task data also available from, http://sccn.ucsd.edu/eeglab/data/headit.html: A 238-channel, single-subject EEG data set recorded at the Swartz Center, UCSD, by Arnaud Delorme, Julie Onton, and Scott Makeig is al. | electrophysiology, data sharing, eeg, visual-auditory cued attention shift paradigm, adult, early adult human, late adult human, memory task, modified sternberg working memory task, visual, auditory, auditory oddball, memory, task |
uses: HED Tags is related to: EEGLAB has parent organization: University of California at San Diego; California; USA |
Normal, Healthy, Others possible | NIMH R01-MH084819; NINDS R01-NS047293 |
Public, Must agree to Data Use Agreement and Terms of Use., Account required for collaboration and to upload data. | nlx_149081 | http://headit-beta.ucsd.edu/, http://sccn.ucsd.edu/eeglab/data/headit.html | http://HeadIT.org | SCR_005657 | Human Electrophysiology Anatomic Data & Integrated Tools (HeadIT) Resource, Human Electrophysiology Anatomic Data & Integrated Tools Resource, Human Electrophysiology Anatomic Data & Integrated Tools, Human Electrophysiology Anatomic Data and Integrated Tools (HeadIT) Resource | 2026-08-11 09:41:10 | 5 | |||
|
PRISM (Stanford database) Resource Report Resource Website 10000+ mentions |
PRISM (Stanford database) (RRID:SCR_005375) | PRISM | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, transcription factor, function, transcription factor binding site, transcription factor regulator, biological role, target gene, target genomic region, genome, FASEB list |
is listed by: OMICtools is listed by: SoftCite is related to: GREAT: Genomic Regions Enrichment of Annotations Tool has parent organization: Stanford University School of Medicine; California; USA |
PMID:23382538 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00489 | SCR_005375 | Predicting Regulatory Information from Single Motifs | 2026-08-11 09:41:17 | 40822 | ||||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | service resource, data or information resource, storage service resource, database, software resource, data repository | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | 2026-08-11 09:41:17 | 32 | ||||||
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TIGRFAMS Resource Report Resource Website 100+ mentions |
TIGRFAMS (RRID:SCR_005493) | JCVI TIGRFAMS, TIGRFAM | data or information resource, database, data set | Consists curated multiple sequence alignments, Hidden Markov Models (HMMs) for protein sequence classification, and associated information designed to support automated annotation of (mostly prokaryotic) proteins. Starting with release 10.0, TIGRFAMs models use HMMER3, which provides excellent search speed as well as exquisite search sensitivity. See the "TIGRFAMs Complete Listing" page to review the accession, protein name, model type, and EC number (if assigned) of all models. TIGRFAMs is a member database in InterPro. The HMM libraries and supporting files are available to download and use for free from our FTP site. | sequence alignment, hidden markov model, protein sequence, classification, protein, protein family, sequence homology, sequence, homology, function, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: InterPro is related to: InterPro has parent organization: J. Craig Venter Institute |
PMID:23197656 | Free | nif-0000-03560, OMICS_01700, biotools:tigrfams | https://bio.tools/tigrfams | http://www.tigr.org/TIGRFAMs | SCR_005493 | TIGRFAMs | 2026-08-11 09:41:17 | 142 | ||||
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Kepler Resource Report Resource Website 10+ mentions |
Kepler (RRID:SCR_005252) | Kepler | software application, workflow software, data processing software, software resource | Kepler is a software application for analyzing and modeling scientific data. Using Kepler''s graphical interface and components, scientists with little background in computer science can create executable models, called scientific workflows, for flexibly accessing scientific data (streaming sensor data, medical and satellite images, simulation output, observational data, etc.) and executing complex analyses on this data. Kepler is developed by a cross-project collaboration led by the Kepler/CORE team. The software builds upon the mature Ptolemy II framework, developed at the University of California, Berkeley. Ptolemy II is a software framework designed for modeling, design, and simulation of concurrent, real-time, embedded systems. The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien��tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging R scripts with compiled C code, or facilitating remote, distributed execution of models. Using Kepler''s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a scientific workflowan executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo��nents developed by the scientific community to address common needs. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. The Kepler Project Leadership Team works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website. | software, workflow |
is listed by: SoftCite is related to: bioKepler has parent organization: University of California at Davis; California; USA has parent organization: University of California at Santa Barbara; California; USA has parent organization: University of California at San Diego; California; USA |
NSF 0722079 | nlx_144278 | SCR_005252 | Kepler Project | 2026-08-11 09:41:05 | 49 | |||||||
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Bambino Resource Report Resource Website 1+ mentions |
Bambino (RRID:SCR_005649) | Bambino | service resource, analysis service resource, software resource, data analysis service, production service resource | A variant detector and graphical alignment viewer for next-generation sequencing data in the SAM/BAM format, which is capable of pooling data from multiple source files. Bambino may be launched online via Java Web Start or downloaded and run locally. | java, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: National Cancer Institute |
PMID:21278191 | Https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/Bambino_Click-thru-agreement-for-executable_final.txt | OMICS_00876, biotools:bambino | https://bio.tools/bambino | SCR_005649 | Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format | 2026-08-11 09:41:10 | 5 | |||||
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TRANSPATH Resource Report Resource Website 1+ mentions |
TRANSPATH (RRID:SCR_005640) | TRANSPATH | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | Database on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices. It can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyzer. Cross-references to important sequence and signature databases such as EMBL/GenBank UniProt/Swiss-Prot InterPro or Ensembl EntrezGene RefSeq are provided. The database is equipped with the tools for data visualization and analysis. It has three modules: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different types of network visualization and hence facilitates understanding; the third is ArrayAnalyzer, which is particularly suited to gene expression array interpretation, and is able to identify key molecules within signalling networks (potential drug targets). These key molecules could be responsible for the coordinated regulation of downstream events. Manual data extraction focuses on direct reactions between signalling molecules and the experimental evidence for them, including species of genes/proteins used in individual experiments, experimental systems, materials and methods. This combination of materials and methods is used in TRANSPATH to assign a quality value to each experimentally proven reaction, which reflects the probability that this reaction would happen under physiological conditions. Another important feature in TRANSPATH is the inclusion of transcription factor-gene relations, which are transferred from TRANSFAC, a database focused on transcription regulation and transcription factors. Since interactions between molecules are mainly direct, this allows a complete and stepwise pathway reconstruction from ligands to regulated genes. | signal transduction, network analyzer, transcriptional regulator, transcription factor, metabolic pathway, signaling pathway, protein-protein interaction, gene-regulatory pathway, signal transduction pathway, complex, signaling molecule, reaction, molecule, gene, pathway, gene expression |
is related to: TRANSFAC is related to: GeneTrail has parent organization: BIOBASE Corporation |
BMBF 031U210B; BMBF 0313092; European Union FP6 contract LSHG-CT-2004-503568; European Union MRTN-CT-2004-512285 |
PMID:18629064 PMID:16381929 PMID:12519957 PMID:11724734 |
Free for academic use, Free for non-profit use, Account required | nif-0000-03580 | http://transpath.gbf.de, http://www.gene-regulation.com/pub/databases.html, http://www.biobase.de/pages/products/databases.html | SCR_005640 | 2026-08-11 09:41:10 | 3 | |||||
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BS Seeker Resource Report Resource Website 1+ mentions |
BS Seeker (RRID:SCR_005641) | data analysis software, software application, software resource, data processing software, sequence analysis software | Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site. | bisulfite sequencing, sequence analysis software, short read, sequence mapping, bio.tools |
uses: Bowtie is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Bs-Seeker2 has parent organization: University of California at Los Angeles; California; USA |
PMID:20416082 | Free, Available for download, Freely available | OMICS_00578, biotools:bs_seeker | https://bio.tools/bs_seeker | SCR_005641 | Bisulfite Sequence Seeker | 2026-08-11 09:41:18 | 3 | ||||||
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1000 Functional Connectomes Project Resource Report Resource Website 10+ mentions |
1000 Functional Connectomes Project (RRID:SCR_005361) | INDI, 1000 FCP, FCP | service resource, project portal, portal, image collection, data or information resource, storage service resource, database, image repository, catalog, data repository | Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets. | resting state functional mri, fmri, brain, neuroimaging, phenotype, function, data sharing, human, mri, r-fmri, rs-fmri, fc-fmri, rs--fcmri, resting-state, dicom, dti, child, adolescent, brain imaging, neuroinformatics, adult human, phenotype, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is used by: MetaSearch is listed by: NITRC-IR is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: NIH Data Sharing Repositories is affiliated with: Preprocessed Connectomes Project is related to: Spanish Resting State Network is related to: NITRC-IR is related to: NIH Data Sharing Repositories is related to: BASH4RfMRI is related to: 1000 Functional Connectomes Project has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: C-PAC is parent organization of: Neuro Bureau - Berlin Mind and Brain Sample is parent organization of: Quiron-Valencia Sample is parent organization of: ABIDE is parent organization of: Consortium for Reliability and Reproducibility is parent organization of: ADHD-200 Sample is parent organization of: FCP Classic Data Sharing Samples is parent organization of: NKI/Rockland Sample is parent organization of: NYU Institute for Pediatric Neuroscience Sample is parent organization of: Virginia Tech Carilion Research Institute Sample is parent organization of: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is parent organization of: Beijing: Eyes Open Eyes Closed Study is parent organization of: Beijing: Short TR Study is parent organization of: COBRE |
NITRIC | PMID:23133413 PMID:23123682 |
Restricted | SCR_015771, nlx_144428, r3d100011565, r3d100011555 | http://www.nitrc.org/projects/fcon_1000/, https://doi.org/10.17616/R3W05R, https://doi.org/10.17616/R35H0H | SCR_005361 | INDI, International Neuroimaging Data-Sharing Initiative, fcon_1000, Functional Connectomes Project International Neuroimaging Data-Sharing Initiative (FCP/INDI), 1000 Functional Connectomes Project, FCP/INDI | 2026-08-11 09:41:07 | 48 |
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