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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PredGPI Resource Report Resource Website 10+ mentions |
PredGPI (RRID:SCR_018363) | web service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource | Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes. | GPI anchored protein predictor, GPI anchored protein, predict presence of GPI anchor, predict position of omega site, discrimination of anchoring signal, prediction of probable omega site, data, screening whole proteome | European Union VI Framework Programme ; FIRB 2003 LIBI–International Laboratory of Bioinformatics |
PMID:18811934 | Free, Freely available | SCR_018363 | 2026-02-14 02:03:37 | 17 | |||||||||
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STARANISO Resource Report Resource Website 50+ mentions |
STARANISO (RRID:SCR_018362) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data. | Anisotropy, diffraction limit, Bayesian estimation, structure amplitude, Global Phasing Limited, anisotropic cut off, data, anisotropic correction data | Global Phasing Consortium | Free, Freely available | SCR_018362 | The STARANISO Server, STARANISO Server, STARANISO server | 2026-02-14 02:03:31 | 70 | |||||||||
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Stan Resource Report Resource Website 100+ mentions |
Stan (RRID:SCR_018459) | software resource, programming language, simulation software, software application | Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest. | Statistical model specification, statistical modeling, statistical computation, log probability function, parameter, data, constant, parameter estimation | DOI:1509.07164 DOI:10.18637/jss.v076.i01 |
Free, Available for download, Freely available | SCR_018459 | 2026-02-14 02:03:35 | 173 | ||||||||||
|
ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | knowledge environment resource, portal, data or information resource, software toolkit, workflow, software resource, narrative resource, training material | Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. | Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | NIBIB P41 EB019936; NSF 1429999; German Federal Ministry of Education and Research |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | 2026-02-14 02:03:21 | 1 | ||||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data visualization software, software resource, data processing software, software application | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-02-14 02:03:39 | 54 | ||||||
|
DAMBE Resource Report Resource Website 1+ mentions |
DAMBE (RRID:SCR_018528) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Natural Science and Engineering Research Council of Canada ; University of Hong Kong ; Hong Kong Research Grant Council |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2026-02-14 02:03:39 | 7 | |||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | web service, data or information resource, data access protocol, software resource, application programming interface | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-02-14 02:03:38 | 2 | |||||||
|
CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data visualization software, data processing software, data analysis software, software application, software resource | Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. | Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization | NSF IIS 1251151 | Free, Available for download, Freely available | SCR_018511 | 2026-02-14 02:03:21 | 10 | ||||||||||
|
piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-14 02:03:42 | 4 | ||||||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet https://bio.tools/GOnet |
SCR_018977 | 2026-02-14 02:03:27 | 3 | |||||||
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Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data processing software, data analysis software, software toolkit, software application, software resource | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-02-14 02:03:44 | 7 | |||||||
|
CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data processing software, data analysis software, software toolkit, software application, software resource | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-02-14 02:03:45 | 22 | |||||||||
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Hetindel Resource Report Resource Website 1+ mentions |
Hetindel (RRID:SCR_018922) | data analysis software, software resource, data processing software, software application | Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels. | Genomic insertions identification, genomic deletions identification, indel, heterozygous sequencing data, alleles, mutation, heterozygous indel, data | has parent organization: Max Planck Institute for Developmental Biology; Tubingen; Germany | Free, Available for download, Freely available | SCR_018922 | 2026-02-14 02:03:42 | 1 | ||||||||||
|
Urinary Stone Disease Research Network Resource Report Resource Website |
Urinary Stone Disease Research Network (RRID:SCR_019059) | USDRN | disease-related portal, data or information resource, portal, topical portal | Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies. | Urinary stone, kidney stone, kidney, treatment, prevention, urologist, nephrologist, pediatrician, clinical trial, data |
is related to: Duke University School of Medicine; North Carolina; USA is related to: University of Pennsylvania; Philadelphia; USA is related to: University of Texas System; Texas; USA is related to: Washington University in St. Louis; Missouri; USA is related to: University of Washington; Seattle; USA |
Kidney stones | NIH ; NIDDK |
Free, Freely available | SCR_019059 | 2026-02-14 02:03:45 | 0 | |||||||
|
COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | data repository, storage service resource, portal, data or information resource, service resource, disease-related portal, topical portal | Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings. | COVID-19, impact data, novel coronavirus global pandemic, novel coronavirus, data |
uses: DataCite is related to: OpenICPSR has parent organization: University of Michigan; Ann Arbor; USA |
COVID-19 | Free, Freely available | https://doi.org/10.3886 https://dx.doi.org/10.3886 |
SCR_019105 | 2026-02-14 02:03:46 | 1 | ||||||||
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Clinical Trials Viewer Resource Report Resource Website |
Clinical Trials Viewer (RRID:SCR_019230) | data access protocol, software resource, web service | Software tool to download and parse information from ClinicalTrials.gov at the time of search to populate the graph of clinical trials. FDA information is updated weekly from Drugs at FDA dataset and FDA postmarketing commitment data set. | Drug, clinical data, clinical trial data, data, ClinicalTrials.gov data, FDA submission, FDA documents, FDA dataset |
is related to: ClinicalTrials.gov has parent organization: McGill University; Montreal; Canada |
Free, Available for download, Freely available | SCR_019230 | 2026-02-14 02:03:47 | 0 | ||||||||||
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TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | data processing software, data analysis software, software toolkit, software application, software resource | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-02-14 02:03:21 | 10 | ||||||
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LION/web Resource Report Resource Website 10+ mentions |
LION/web (RRID:SCR_017018) | Lipid Ontology (LION) | web application, data analysis service, analysis service resource, production service resource, service resource, software resource | Web based ontology enrichment tool for lipidomic data analysis. Used for lipidomics to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations. Freely accessible in a platform independent way. | lipid, ontology, enrichment, lipidomic, data, analysis, biophysical | is related to: Utrecht University; Utrecht; Netherlands | DOI:10.1101/398040 | Free, Freely available | SCR_017018 | The Lipid Ontology (LION), Lipid Ontology, LIpid ONtology (LION), LIpid ONtology, LION | 2026-02-14 02:03:22 | 21 | |||||||
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Anima Resource Report Resource Website 10+ mentions |
Anima (RRID:SCR_017017) | registration software, diffusion-weighted mri 3d image, data processing software, mri 3d image, 3d spatial image, portal, data or information resource, data analysis software, software toolkit, software application, image, image processing software, software resource, image analysis software | Portal provides software library and python scripts for medical image processing. Open source set of software tools for medical image processing, medical image analysis, image registration, statistical analysis, quantitative MRI processing, image denoising and filtering, and segmentation developed by VISAGES/Empenn research team. Available as Github repository and compiled binaries for various OS including OSX, Fedora, Ubuntu, Windows. | medical, image, processing, analysis, registration, statistical, quantitative, MRI, data, VISAGES |
is related to: Anima scripts is related to: Empenn has parent organization: VISAGES Research |
Free, Freely available, Available for download | http://olivier.commowick.org/software_anima.php | SCR_017017 | 2026-02-14 02:03:13 | 15 | |||||||||
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GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data analysis software, software resource, data processing software, software application | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-02-14 02:03:08 | 50 |
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