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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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MS Amanda Resource Report Resource Website 1+ mentions |
MS Amanda (RRID:SCR_018396) | software application, data processing software, algorithm resource, software resource, data analysis software | Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria. | Tandem mass spectrometry, protein database, scoring system, peptide identification, data, search algorithm, protein identification algorithm, peptide identification, proteomic | is related to: PeptideShaker | Austrian Science Fund ; European Community Seventh Framework Programme ; MeioSys |
PMID:24909410 | Free, Available for download, Freely available | https://ms.imp.ac.at/?goto=msamanda | SCR_018396 | MS Amanda 2.0, Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra | 2026-02-15 09:22:21 | 2 | ||||||
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Interactive Dotplot Resource Report Resource Website 1+ mentions |
Interactive Dotplot (RRID:SCR_018329) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets. | Customized interactive graphic, univariate scatterplot, box plot, violin plot, continuous variable comparing, across different study group, subgroup visualization, subgroup cluster, non independent data visualization, data, data set | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018329 | 2026-02-15 09:21:35 | 1 | |||||||||
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Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | software resource, data access protocol, web service, data or information 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 | 2026-02-15 09:22:21 | 2 | |||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | software application, data visualization software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:21:38 | 10 | ||||||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software application, data processing software, data analysis software, software resource | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-02-15 09:22:21 | 25 | ||||||||
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TinderMIX Resource Report Resource Website 1+ mentions |
TinderMIX (RRID:SCR_018364) | software application, data processing software, data analysis software, software resource | Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features. | Dose dependent gene expression, time dependent gene expression, gene expression analysis, dose response, cluster gene expression, contour plot, toxicogenomics data analysis, time point, dose level, expression pattern identification, data | Free, Available for download, Freely available | https://rdrr.io/github/angy89/TinderMIX/ https://github.com/angy89/TinderMIX/ |
SCR_018364 | Time-Dose INtegrated moDelling of toxicogenomics data | 2026-02-15 09:21:36 | 1 | |||||||||
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PredGPI Resource Report Resource Website 10+ mentions |
PredGPI (RRID:SCR_018363) | software resource, data access protocol, web service, service resource, production service resource, data or information resource, analysis service 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 | 2026-02-15 09:22:14 | 17 | |||||||||
|
STARANISO Resource Report Resource Website 50+ mentions |
STARANISO (RRID:SCR_018362) | software resource, data access protocol, web service, service resource, production service resource, analysis service 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 | 2026-02-15 09:22:13 | 70 | |||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | software resource, data access protocol, web service, service resource, production service resource, analysis service 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 | 2026-02-15 09:22:23 | 4 | ||||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | software application, data visualization software, data processing software, software resource | 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 | 2026-02-15 09:22:22 | 54 | ||||||
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DAMBE Resource Report Resource Website 1+ mentions |
DAMBE (RRID:SCR_018528) | software application, sequence analysis software, data processing software, software resource, data analysis software | 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 | 2026-02-15 09:22:14 | 7 | |||||
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GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | software resource, data access protocol, web service, service resource, production service resource, analysis service 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 | 2026-02-15 09:22:25 | 3 | |||||||
|
Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | software application, data processing software, software resource, software toolkit, data analysis software | 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 | 2026-02-15 09:22:26 | 7 | |||||||
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CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | software application, data processing software, software resource, software toolkit, data analysis software | 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 | 2026-02-15 09:22:26 | 22 | |||||||||
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Hetindel Resource Report Resource Website 1+ mentions |
Hetindel (RRID:SCR_018922) | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:19 | 1 | ||||||||||
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Urinary Stone Disease Research Network Resource Report Resource Website |
Urinary Stone Disease Research Network (RRID:SCR_019059) | USDRN | disease-related portal, topical portal, data or information resource, 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 | 2026-02-15 09:21:47 | 0 | |||||||
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COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | portal, service resource, storage service resource, data repository, data or information resource, topical portal, disease-related 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 | 2026-02-15 09:22:27 | 1 | ||||||||
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Clinical Trials Viewer Resource Report Resource Website |
Clinical Trials Viewer (RRID:SCR_019230) | web service, data access protocol, software resource | 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 | 2026-02-15 09:22:21 | 0 | ||||||||||
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Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | software application, image processing software, data processing software, software resource, software toolkit | Software package for image processing for MATLAB. Used for processing of calcium imaging data. | Image processing, data, calcium imaging data, calcium imaging |
is used by: IRIS two photon acquisition package is related to: MATLAB |
Swiss National Science Foundation ; Novartis Research Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021213 | 2026-02-15 09:22:31 | 1 | ||||||||
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Cerebrovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) | CDKP | portal, database, data or information resource, topical portal, disease-related portal | Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data. | human, genetic, information, cerebrovascular, disease, data, knowledge |
is listed by: NIDDK Information Network (dkNET) has parent organization: Massachusetts General Hospital Labs and Facilities |
cerebrovascular disease | NINDS ; NIH ; Accelerating Medicines Partnership in Type 2 Diabetes |
Free, Available for download | SCR_016535 | SCR_015628 | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-02-15 09:21:34 | 14 |
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