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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ODAM Resource Report Resource Website 1+ mentions |
ODAM (RRID:SCR_018774) | data management software, data access protocol, software application, web service, software repository, software resource | Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users. | Experimental data tables, research data management, OpenAPI, FAIR Data principles, assessment, EDTMS, data management, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:ODAM, biotools:ODAM | https://bio.tools/ODAM, https://bio.tools/ODAM, https://bio.tools/ODAM, https://bio.tools/ODAM | SCR_018774 | Open Data for Access and Mining | 2026-08-13 09:30:16 | 3 | |||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | data analysis software, data processing software, software application, analysis service resource, production service resource, service resource, software resource | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-08-13 09:30:17 | 463 | ||||||||
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Scalable Analytics for Brain Exploration Research Resource Report Resource Website 1+ mentions |
Scalable Analytics for Brain Exploration Research (RRID:SCR_018812) | SABER, saber | data processing software, software application, software toolkit, software library, workflow software, software resource | Library of containerized tools and workflow deployment system for enabling processing of large neuroimaging datasets. Provides canonical neuroimaging workflows specified in standard workflow language (CWL), integration with workflow execution engine (Airflow), imaging database (bossDB), and parameter database (Datajoint) to deploy workflows at scale, and tools to automate deployment and optimization of neuroimaging pipelines. | Running containerized workflow, large neuroimaging datasets, canonical neuroimaging workflow, neuroimaging pipeline deployment, neuroimaging pipeline optimization | is related to: Brain Observatory Storage Service and Database (BossDB) | NIMH R24 MH114799 | DOI:10.1101/615161v1.full | Free, Available for download, Freely available | SCR_018812 | 2026-08-13 09:30:16 | 1 | |||||||
|
PHD SECONDARY STRUCTURE Resource Report Resource Website 1+ mentions |
PHD SECONDARY STRUCTURE (RRID:SCR_018778) | data access protocol, software resource, service resource, web service | Web tool for secondary structure prediction. Used for network protein sequence analysis. | Secondary structure prediction, network protein, protein sequence analysis, protein sequence, secondary structure predictor | Free, Freely available | SCR_018778 | 2026-08-13 09:30:16 | 2 | |||||||||||
|
Muscle X Resource Report Resource Website 1+ mentions |
Muscle X (RRID:SCR_018811) | data analysis software, data processing software, software application, software toolkit, image analysis software, software resource | Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data. | Diffraction analysis, x ray image, diffraction X-Ray image analysis, X-ray data, X-ray fiber diffraction data, data analysis, data reduction | has parent organization: Illinois Institute of Technology; Illinois; USA | Free, Available for download, Freely available | https://sourceforge.net/projects/musclex/files/ | SCR_018811 | MuscleX, Muscle X 1.14.12 | 2026-08-13 09:30:30 | 5 | ||||||||
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Trinotate Resource Report Resource Website 10+ mentions |
Trinotate (RRID:SCR_018930) | data analysis software, data processing software, software application, software toolkit, software resource | Software annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. | Automatic functional annotation, transcriptome annotation, de novo assembled transcriptome, model organism, non model organism | Free, Available for download, Freely available | SCR_018930 | Transcriptome Functional Annotation and Analysis | 2026-08-13 09:30:11 | 37 | ||||||||||
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PSORT II Resource Report Resource Website 10+ mentions |
PSORT II (RRID:SCR_018772) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web tool for prediction of protein sorting signals and localization sites in amino acid sequencies. Recommended for animal/yeast sequences. Analyzes input sequence by applying stored rules for various sequence features of known protein sorting signals to report possiblity for input protein to be localized at each candidate site with additional information. | Protein sorting signal prediction, protein localization site, localization site prediction, amino acid sequence, sequence analysis, protein sorting signal | is related to: Psort | Free, Freely available | https://psort.hgc.jp/, https://www.psort.org/ | SCR_018772 | prediction of protein sorting signals and localization sites in amino acid sequencies, psort2, psort II | 2026-08-13 09:30:08 | 49 | ||||||||
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DoubletFinder Resource Report Resource Website 1000+ mentions |
DoubletFinder (RRID:SCR_018771) | data analysis software, data processing software, software resource, software application | Software R package that predicts doublets in single cell RNA sequencing data. Doublet detection in single cell RNA sequencing data using artificial nearest neighbors. Identifies doublets using only gene expression data. | Doublet detection in single cell RNA, single cell RNA, doublet detection, RNA sequencing data, gene expression data, artificial nearest neighbors |
is related to: Seurat has parent organization: University of California at San Francisco; California; USA |
Department of Defense Breast Cancer Research Program ; NICHD DP2 HD080351; NSF MCB 1330864; UCSF Center for Cellular Construction ; NSF Science and Technology Center ; Damon Runyon Cancer Research Foundation |
PMID:30954475 | Free, Available for download, Freely available | SCR_018771 | 2026-08-13 09:30:16 | 1250 | ||||||||
|
RAPIDO Resource Report Resource Website 1+ mentions |
RAPIDO (RRID:SCR_018935) | data processing software, data access protocol, software application, image analysis software, alignment software, web service, software resource | Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains. | Protein structure alignment, rapid alignment, protein domain, conformational changes presence, 3D alignment, crystal structure, protein molecule, conformational change presence, identify structural region, distant sequence, movable domains | European Molecular Biology Laboratory ; Associazione Italiana per la Ricerca sul Cancro |
PMID:18460546 PMID:18727838 |
Free, Freely available | SCR_018935 | Rapid Alignment of Proteins in terms of Domains, Rapid alignment of proteins in terms of domains | 2026-08-13 09:30:11 | 2 | ||||||||
|
UCSC Xena Resource Report Resource Website 1000+ mentions |
UCSC Xena (RRID:SCR_018938) | data or information resource, data access protocol, analysis service resource, production service resource, service resource, web service, software resource, portal | Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. | Data visualization, data analysis, genomics data, explore functional genomic data, functional genomic, data sets, genomic variable correlation, phenotypic variables correlation | has parent organization: University of California at Santa Cruz; California; USA | Free, Freely available | https://xenabrowser.net/ | SCR_018938 | UCSC Xena Browser, Xena Browser | 2026-08-13 09:30:11 | 4804 | ||||||||
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QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | data analysis software, data processing software, software application, software toolkit, software resource | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-08-13 09:30:06 | 27 | ||||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data analysis software, data processing software, software application, software toolkit, software resource | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-08-13 09:30:14 | 21 | |||||||
|
AsPredicted Resource Report Resource Website 100+ mentions |
AsPredicted (RRID:SCR_018789) | topical portal, data or information resource, portal | Website for study pre-registration. Defines minimum required criteria for pre-registration and allows authors to pre-register their study. It is standardized pre-registration that requires only what is necessary to separate exploratory from confirmatory analyses. | Study pre-registration, publish paper, evaluation, minimum required criteria, author study pre-registration, standardized pre-registration | has parent organization: University of Pennsylvania; Philadelphia; USA | Restricted | SCR_018789 | 2026-08-13 09:30:16 | 165 | ||||||||||
|
AlgPred Resource Report Resource Website 50+ mentions |
AlgPred (RRID:SCR_018780) | data access protocol, software resource, service resource, web service | Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes. | Allergen prediction, allergenic protein, allergenic protein prediction, IgE epitopes mapping, epitope, protein region, prediction, bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research | PMID:16844994 | Free, Freely available | biotools:algpred | https://webs.iiitd.edu.in/raghava/algpred/submission.html, https://bio.tools/algpred | SCR_018780 | 2026-08-13 09:30:29 | 94 | ||||||
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FunGene Resource Report Resource Website 50+ mentions |
FunGene (RRID:SCR_018749) | data or information resource, software toolkit, analysis service resource, production service resource, database, service resource, data repository, storage service resource, software resource | Functional gene pipeline and repository. Functional gene repository provides collections of genes in interactive platform, while functional gene pipeline offers suite of tools for functional gene amplicon processing and analysis. Together they enable key steps in functional gene based microbial community analysis, from target selection and primer analysis to amplicon processing and ecological discovery. | Gene processing, microbial ecology, functional genes, amplification primers, phylogeny, biogeochemical cycles, amplicon analysis, ecological discovery, microbial community | has parent organization: Michigan State University; Michigan; USA | NIEHS P42 ES004911; USDA National Institute of Food and Agriculture ; NIDDK UH3 DK083993; Office of Science U.S. Department of Energy ; NIEHS |
PMID:24101916 | Free, Freely available | SCR_018749 | FunGene Pipeline | 2026-08-13 09:30:08 | 58 | |||||||
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NanoGalaxy Resource Report Resource Website 10+ mentions |
NanoGalaxy (RRID:SCR_018912) | data analysis software, data processing software, data access protocol, software application, software toolkit, data visualization software, web service, software resource | Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance. | European Galaxy Project, Oxford Nanopore Technologies, Oxford Nanopore Technologies data, data analysis, long reads technology, ONT oriented tools collection, custom Galaxy instance, , Galaxy, Nanopore, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy is related to: University of Freiburg; Baden-Wurttemberg; Germany |
Free, Freely available | biotools:nanogalaxy | https://galaxyproject.org/use/nanogalaxy/, https://bio.tools/nanogalaxy | SCR_018912 | 2026-08-13 09:30:31 | 10 | ||||||||
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BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | software application, software toolkit, software library, code testing framework, software resource, software development tool | Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes. | Electronic Health Record, electronic health record data generation, health data, testing health data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:badmedicine | https://bio.tools/badmedicine | SCR_018879 | 2026-08-13 09:30:10 | 1 | ||||||||
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robvis Resource Report Resource Website 100+ mentions |
robvis (RRID:SCR_018755) | robvis | web application, software resource, software toolkit | Software R package and web app, which facilitates rapid production of publication quality risk of bias assessment figures. Used to produce high quality figures that summarize the risk-of-bias assessments performed as part of systematic review or research synthesis project. | Risk of bias assessment, publication figure, publication quality figure, figure production, systematic review, research synthesis project | is related to: Shiny | University of Bristol ; University Hospitals Bristol NHS Foundation Trust |
DOI:10.1002/jrsm.1411 | Free, Freely available | SCR_018755 | Risk Of Bias VISualization | 2026-08-13 09:30:08 | 100 | ||||||
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scTHI Resource Report Resource Website 1+ mentions |
scTHI (RRID:SCR_018918) | scTHI | data analysis software, data processing software, software resource, software application | Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment. | Ligand receptor, active pair, active pair ligand receptor, single cell, tumor interaction, tumor microenvironment, cells clasification | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018918 | 2026-08-13 09:30:31 | 1 | |||||||||
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T2DSystems Resource Report Resource Website 1+ mentions |
T2DSystems (RRID:SCR_018913) | topical portal, data or information resource, organization portal, project portal, disease-related portal, consortium, portal | Project to bridge gap between in vitro human islet studies and clinical studies in human subjects. Used to integrate cellular and medical research data, collected by partners, with computational modelling to identify pathophysiological mechanisms and markers of spectrum of biological and cellular processes involved in pancreatic beta cell failure leading to impaired glucose tolerance and T2D. | Human islet study, cellular data, medical data, diabetes, pancreatic beta cell failure, impaired glucose tolerance, type 2 diabetes, glucose tolerance | is related to: TIGER Data Portal | Type 2 Diabetes | EU Horizon 2020 | Restricted | SCR_018913 | Type 2 Diabetes Systems, T2DSystems | 2026-08-13 09:30:17 | 1 |
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