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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RDPipeline Resource Report Resource Website 10+ mentions |
RDPipeline (RRID:SCR_001192) | RDPipeline | data processing software, software application, software resource | Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available. | amplicon sequencing, high-throughput sequencing, rrna, assembly, quality filtering, taxonomy, analysis, FASEB list |
is listed by: OMICtools has parent organization: Ribosomal Database Project |
PMID:24288368 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02158 | SCR_001192 | RDP Pipeline, RDP Amplicon Sequence Pipeline | 2026-09-12 01:00:52 | 39 | ||||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882; Wellcome Trust WT082930MA |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-09-12 01:00:18 | 8 | ||||||
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Coronavirus Immunotherapy Consortium Resource Report Resource Website 10+ mentions |
Coronavirus Immunotherapy Consortium (RRID:SCR_018258) | CoVIC | consortium, data or information resource, organization portal, portal, topical portal | Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. | COVID-19, antibody, antibody based therapy, coronavirus, SARS-CoV-2, antibody collection, analysis, potency in vitro, efficacy in vivo, standardized assay, identify mAb, therapeutic molecule, vulnerable population protect, database, data |
is related to: La Jolla Institute for Immunology is related to: Duke University; North Carolina; USA is related to: CoVIC-DB Database |
COVID-19 | Free, Freely available | SCR_018258 | 2026-09-12 01:00:21 | 14 | ||||||||
|
ClusPro Resource Report Resource Website 500+ mentions |
ClusPro (RRID:SCR_018248) | data access protocol, service resource, software resource, web service | Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results. | Protein-protein docking, protein structure, energy function, energy parameter selection, analysis, data |
has parent organization: Boston University; Massachusetts; USA has parent organization: Stony Brook University; New York; USA |
NIGMS R01 GM061867; NIGMS R35 GM118078 |
PMID:28079879 | Free, Freely available | SCR_018248 | ClusPro 2.0 | 2026-09-12 01:00:21 | 979 | |||||||
|
PEAKS Studio Resource Report Resource Website 10+ mentions |
PEAKS Studio (RRID:SCR_022841) | software resource | Software platform with complete solutions for discovery proteomics, including protein identification and quantification, analysis of post translational modifications and sequence variants (mutations), and peptide/protein de novo sequencing. | Bioinformatics Solutions Inc., peptide de novo sequencing, mass spectrometry, discovery proteomics, protein identification and quantification, analysis, post translational modifications, sequence variants, mutations, | PMID:14558135 | Restricted | SCR_022841 | PEAKS Studio Xpro | 2026-09-12 01:00:30 | 18 | |||||||||
|
PopTools Resource Report Resource Website 10+ mentions |
PopTools (RRID:SCR_022840) | software resource | Software to allow construction, analysis, and simulation of complex models in spreadsheet format. | construction, analysis, simulation, complex models, spreadsheet format | Free, Available for download, Freely available | https://www.maa.org/press/periodicals/loci/resources/poptools | SCR_022840 | 2026-09-12 01:00:30 | 49 | ||||||||||
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CoVIC-DB Database Resource Report Resource Website 1+ mentions |
CoVIC-DB Database (RRID:SCR_018339) | CoVIC-DB | catalog, data or information resource, database | Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics. | SARS-CoV-2, monoclonal antibodies, antibody, antibody contribution, analysis, antibody based immunotherapy, COVID-19, COVID-19 data | is related to: Coronavirus Immunotherapy Consortium | COVID-19 | Bill and Melinda Gates Foundation ; Wellcome and MasterCard Impact Fund |
Free, Freely available | SCR_018339 | Coronavirus Immunotherapy Consortium Database | 2026-09-12 01:00:36 | 2 | ||||||
|
REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | software resource, web application | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-09-12 01:00:35 | 23733 | |||||
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SBIA Resource Report Resource Website 1+ mentions |
SBIA (RRID:SCR_013628) | SBIA | access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher. | effect, alzheimer's, analysis, anatomical, biomedical, biophysical, brain, cancer, breast cancer, cardiac, classification, clinical, computer, deformation, dimensional, disease, method, model, mouse, organ, pattern, prostate, registration, schizophrenia, segmentation, statistical analysis, study, treatment, image | has parent organization: University of Pennsylvania; Philadelphia; USA | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-33052 | SCR_013628 | The Section for Biomedical Image Analysis, Section for Biomedical Image Analysis | 2026-09-12 01:00:36 | 4 | |||||||
|
Harmony Resource Report Resource Website 10+ mentions |
Harmony (RRID:SCR_018809) | data acquisition software, data processing software, image acquisition software, image analysis software, software application, software resource | Harmony high content imaging and analysis software. Used to quantify complex cellular phenotypes. Designed for PerkinElmer high content screening systems. | Imaging, analysis, cellular phenotype quantification, PerkinElmer, high content, screening system, cell phenotypic screening, live cell imaging, | is related to: Perkin Elmer: Operetta CLS | Restricted | SCR_018809 | Harmony 4.8 | 2026-09-12 12:59:06 | 34 | |||||||||
|
RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, data processing software, software application, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
Berlin Institute for Medical Systems Biology ; NIGMS R01 GM104962 |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | 2026-09-12 12:59:06 | 8 | ||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-09-12 12:59:08 | 4 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | 2026-09-12 12:59:08 | 1 | ||||||||
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TwoSampleMR Resource Report Resource Website 500+ mentions |
TwoSampleMR (RRID:SCR_019010) | data analysis software, data processing software, software application, software resource | Software R package for performing Mendelian randomization using genome wide association study summary data. | GWAS data, genome wide associated study data, genome data, Mendelian randomization, analysis | PMID:29846171 | Free, Available for download, Freely available | SCR_019010 | 2026-09-12 12:59:08 | 732 | ||||||||||
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HeteroAnalysis Resource Report Resource Website 50+ mentions |
HeteroAnalysis (RRID:SCR_014991) | algorithm resource, data analysis software, data processing software, software application, software resource | Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved. | sedimentation equilibrium, ultracentrifugation, analysis, model dependent | has parent organization: University of Connecticut; Connecticut; USA | Available for download | http://core.uconn.edu/files/auf/ha-help/HA-Help.htm | SCR_014991 | HeteroAnalysis Version 1.1.0.58 | 2026-09-12 12:58:24 | 62 | ||||||||
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MetaboAnalyst Resource Report Resource Website 10000+ mentions |
MetaboAnalyst (RRID:SCR_015539) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for statistical, functional and integrative analysis of metabolomics data. Web based tool suite used for metabolomic data processing, normalization, multivariate statistical analysis, and data annotation, biomarker discovery and classification. | statistical, functional, integrative, analysis, metabolomics, data, processing, annotation, biomarker, discovery |
is listed by: SoftCite has parent organization: McGill University; Montreal; Canada has parent organization: University of Alberta; Alberta; Canada |
Alberta Ingenuity Fund ; Alberta Life Sciences Institute ; Canada Research Chairs Program ; Canadian Institutes for Health Research ; Genome Alberta ; Genome Canada ; McGill University ; Natural Sciences and Engineering Research Council of Canada |
PMID:29762782 | Free, Available for download, Freely available, Tutorial available, Acknowledgement requested | SCR_016717 | http://old.metaboanalyst.ca/MetaboAnalyst/ | SCR_015539 | MetaboAnalyst 4.0, MetaboAnalyst 3.0 | 2026-09-12 12:58:27 | 13689 | |||||
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CalR Resource Report Resource Website 100+ mentions |
CalR (RRID:SCR_015849) | data analysis software, data processing software, data visualization software, software application, software resource, web application | A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates. | indirect, calorimerty, analysis, visualization, energy, balance, food intake, energy expenditure, metabolism, metabolic phenotyping, CLAMS, PhenoMaster, Prometheon, biostatistics, ANCOVA, reproducibility, Columbus Instruments, Sable Systems, TSE | is related to: Harvard University; Cambridge; United States | Harvard Digestive Disease Center ; Mouse Metabolic Phenotyping Center ; NIDDK |
DOI:10.1101/213967 | Freely available, Public | https://calrapp.org | SCR_015849 | A Web Application for Indirect Calorimetry Analysis | 2026-09-12 12:58:31 | 228 | ||||||
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BIAevaluation Software Resource Report Resource Website 100+ mentions |
BIAevaluation Software (RRID:SCR_015936) | data analysis software, data processing software, data visualization software, software application, software resource, standalone software | Analysis software for life science data. This software package is for presentation and evaluation of sensorgram data from real-time BIA analyses. | evaluation, life, science, bia, biacore, sensorgram, bia, analysis, real-time | Commercially Available, Available for purchase, License available for purchase | http://www.molecular-interactions.si/data/equipment/BIAeval3-AC.pdf | SCR_015936 | BIAevaluation Software Kit, BIAevaluation | 2026-09-12 12:58:32 | 459 | |||||||||
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Pattern Component Modelling Toolbox Resource Report Resource Website 1+ mentions |
Pattern Component Modelling Toolbox (RRID:SCR_015891) | PCM | data analysis software, data processing software, software application, software resource | Software for a Bayesian approach for evaluating representational models that specify how complex patterns of neural activity relate to visual stimuli, motor actions, or abstract thoughts. PCM evaluates the ability of models to predict novel brain activity patterns and integrates over all possible activity profiles and computes the marginal likelihood of the data under the activity profile distribution specified by the representational model. | bayesian, representational, model, motor, abstract, visual, encoding, neural, imaging, activity, pattern, analysis, voxel | James McDonnell Foundation ; JSPS 15J03233; NSERC RGPIN-2016-04890 |
PMID:28843540 | Free, Available for download | SCR_015891 | Pattern component modeling (PCM), PCM Toolbox, Pattern Component Modeling toolbox for multivariate analysis | 2026-09-12 12:58:32 | 3 | |||||||
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Varian Medical Systems, Inc. Resource Report Resource Website 10+ mentions |
Varian Medical Systems, Inc. (RRID:SCR_017372) | commercial organization | Manufacturer located in Palo Alto, California, USA, that has made developments in fields of radiotherapy, radiosurgery, X-ray tube technology, digital image detectors, cargo screening, and non-destructive testing. Varian technology and software for processing diagnostic X-ray images is being used in radiotherapy and analysis. | Manufacturer, commercial, company, component, radiotherapy, spectrometry, software, analysis, therapy, medical, imaging, technology, development | grid.482350.8, ISNI: 0000 0004 0482 3442, Wikidata: Q30343843 | https://ror.org/049tb1q96 | SCR_017372 | Varian | 2026-09-12 12:58:52 | 13 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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