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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Omics Discovery Index Resource Report Resource Website 10+ mentions |
Omics Discovery Index (RRID:SCR_010494) | OmicsDI, DDI, DDICC | data or information resource, portal, database | Portal for dataset discovery across a heterogeneous, distributed group of transcriptomics, genomics, proteomics and metabolomics data resources. These resources span eight repositories in three continents and six organisations, including both open and controlled access data resources. | dataset search, knowledge framework, knowledge discovery |
is affiliated with: MetabolomeXchange is affiliated with: ProteomeXchange has parent organization: University of California at San Diego; California; USA is parent organization of: Integrated Datasets |
NIA 1U24AI117966-01; NIGMS 1U54GM114833-01 |
Free, Public | nlx_158507, SCR_014747 | SCR_010494 | Omics Discovery Index (OmicsDI) | 2026-02-14 02:05:34 | 27 | ||||||
|
BALBES Resource Report Resource Website 1+ mentions |
BALBES (RRID:SCR_018763) | software resource, software toolkit, software application, standalone software | Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement. | Molecular replacement pipeline, protein structure, solving protein structure, x-ray crystallographic data, molecular replacement, molecular replacement in CCP4, solving crystal structure, automated system, no user intervention, model searching, refinement |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: CCP4 |
Wellcome Trust ; NIGMS R01 GM069758 |
PMID:18094476 | Free, Available for download, Freely available | SCR_018763 | 2026-02-14 02:05:44 | 1 | ||||||||
|
SViCT Resource Report Resource Website 1+ mentions |
SViCT (RRID:SCR_023656) | data analysis software, software resource, data processing software, software application | Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA. | detecting structural variations, cell free DNA, cfDNA, circulating tumor DNA low dilutions, ctDNA | Natural Sciences and Engineering Research Council Discovery Grant ; Terry Fox Research Institute New Frontiers Program Project Grant ; Natural Sciences and Engineering Research Council Discovery Frontiers Program ; National Science Foundation ; NIGMS GM108348; Indiana University Grant Challenges Program ; Precision Health Initiative |
PMID:30759232 | Free, Available for download, Freely available | SCR_023656 | Structural Variant detection in Circulating Tumor DNA | 2026-02-14 02:05:08 | 1 | ||||||||
|
CRISPRscan Resource Report Resource Website 50+ mentions |
CRISPRscan (RRID:SCR_023777) | data access protocol, software resource, web service | Web tool for predictive sgRNA-scoring that captures sequence features affecting Cas9/sgRNA activity in vivo. Scoring algorithm to help select the best gRNAs for CRISPR. | predictive sgRNA-scoring, sequence features capture, affecting Cas9/sgRNA activity in vivo, select gRNAs for CRISPR, | has parent organization: Yale University; Connecticut; USA | Swiss National Science Foundation ; NICHD R21 HD073768; NIGMS R01 GM103789; NIGMS R01 GM102251; NIGMS R01 GM101108; NIGMS GM081602; NICHD R01 HD081379; Edward Mallinckrodt Jr Foundation |
Free, Freely available | SCR_023777 | 2026-02-14 02:05:14 | 58 | |||||||||
|
PathVisio Resource Report Resource Website 10+ mentions |
PathVisio (RRID:SCR_023789) | data visualization software, data processing software, software toolkit, software application, software resource | Software visualization tool for biological pathways. Pathway analysis and drawing software which allows drawing, editing, and analyzing biological pathways. Developed in Java and can be extended with plugins. | biological pathway editor, pathway editor, visualization and analysis, extendable pathway analysis, | NIGMS R01 GM100039; Netherlands Consortium for Systems Biology ; NIGMS GM080223; NHGRI HG003053; Transnational University Limburg |
PMID:25706687 PMID:18817533 |
Free, Available for download, Freely available | SCR_023789 | PathVisio 3 | 2026-02-14 02:05:01 | 24 | ||||||||
|
PERFect Resource Report Resource Website |
PERFect (RRID:SCR_024682) | software resource, data processing software, software application | Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering. | filtering test, microbiome data, microbiome data processing, | NSF ; NIGMS 1U54GM104944 |
PMID:29917060 | Free, Available for download, Freely available | SCR_024682 | Permutation Filtering Package in R | 2026-02-14 02:05:10 | 0 | ||||||||
|
WebProtege Resource Report Resource Website 1+ mentions |
WebProtege (RRID:SCR_024627) | software resource, web application | Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat. | editing biomedical ontologies, editing OWL 2 ontologies, ontology editor, OBO ontologies, |
has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Biomedical Informatics Research |
NIGMS GM103316 | PMID:24771560 | Free, Freely available | https://protegewiki.stanford.edu/wiki/WebProtege | SCR_024627 | WebProtégé | 2026-02-14 02:05:09 | 2 | ||||||
|
Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | data processing software, data analysis software, software toolkit, software application, software resource | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NIGMS GM085764; NIDDK DK091183; NHLBI R00 123485 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-02-14 02:04:24 | 608 | ||||||||
|
3DRefine Resource Report Resource Website 10+ mentions |
3DRefine (RRID:SCR_021883) | data access protocol, software resource, web service | Interactive web server for efficient protein structure refinement with capability to perform web based statistical and visual analysis. | efficient protein structure refinement, statistical and visual analysis | NIGMS R01 GM093123 | DOI:10.1093/nar/gkw336 | Free, Freely available | SCR_021883 | 2026-02-14 02:04:42 | 20 | |||||||||
|
GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data analysis software, software resource, data processing software, software application | Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | power, multivariate, linear, models, Gaussian, error, Java, web, calculate | NIGMS R01 GM121081; NIGMS R25 GM111901; NLM G13 LM011879 |
PMID:24403868 PMID:40901910 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016297 | , GLIMMPSE Version 3 | 2026-02-14 02:04:57 | 8 | ||||||||
|
CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | data processing software, data analysis software, data analytics software, software toolkit, software application, software resource | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI134713; NIAID R21 AI142667; NIAID R01 AI134246; NIAID R01 AI076327; NIAID U19 AI135976; NIAID T32 AI10667; NIGMS T32 GM007270; NICHD T32 HD007233; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-02-14 02:04:59 | 22 | |||||||
|
STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data visualization software, software resource, data processing software, software application | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | 2026-02-14 02:04:36 | 4 | |||||||||
|
SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | data analysis software, software resource, data processing software, software application | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-02-14 02:05:03 | 15 | |||||||
|
ZDOCK Server Resource Report Resource Website 50+ mentions |
ZDOCK Server (RRID:SCR_022518) | data access protocol, software resource, web service | Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. | Protein docking server, ZDOCK, M-ZDOCK, predict structures, protein-protein complexes, symmetric multimers | NIGMS GM084884 | PMID:24532726 | Free, Freely available | SCR_022518 | 2026-02-14 02:04:56 | 75 | |||||||||
|
sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | 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 | 2026-02-14 02:05:02 | 6 | ||||||||
|
VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | data access protocol, software resource, web service | 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 | 2026-02-14 02:04:45 | 2 | ||||||||
|
Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | data analysis software, software resource, data processing software, software application | Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. | quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, | NIGMS R01GM118568; NIGMS R01GM121459; UK Medical Research Council |
PMID:33693500 | Free, Available for download, Freely available | https://bioconductor.org/packages/megadepth | SCR_022779 | 2026-02-14 02:04:58 | 2 | ||||||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | data or information resource, ontology, controlled vocabulary | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/ http://bioportal.bioontology.org/ontologies/ECO |
SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-02-14 02:05:01 | 19 | |||||
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trRosetta Resource Report Resource Website 50+ mentions |
trRosetta (RRID:SCR_021181) | software resource, simulation software, service resource, software application | Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets. | protein structure, restraint-guided structure generation, protein structure prediction | uses: Rosetta | National Natural Science Foundation of China ; Fok Ying-Tong Education Foundation ; Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ; Thousand Youth Talents Plan of China ; China Scholarship Council ; NIGMS R01 GM092802; NIH Office of the Director DP5 OD026389 |
PMID:31896580 | Free, Freely available | https://github.com/gjoni/trRosetta | SCR_021181 | transformed restrained Rosetta | 2026-02-14 02:04:37 | 67 | ||||||
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SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | software resource, data processing software, data acquisition software, software application | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-02-14 02:03:23 | 213 |
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