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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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SqueezeMeta Resource Report Resource Website 10+ mentions |
SqueezeMeta (RRID:SCR_021821) | data processing software, software application, data analysis software, software resource | Software tool as fully automated pipeline for metagenomic analysis. Used for metagenomics covering all steps of analysis. Features several characteristics including co-assembly procedure or co-assembly of unlimited number of metagenomes via merging of individual assembled metagenomes, both with read mapping for estimation of abundances of genes in each metagenome. Includes binning and bin checking for retrieving individual genomes. | automated metagenomics pipeline, metagenomics analysis steps, metagenomic analysis | Spanish Ministry of Economy and Competitiveness. | DOI:10.3389/fmicb.2018.03349 | Free, Available for download, Freely available | SCR_021821 | 2026-08-14 09:28:32 | 20 | |||||||||
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CIRCexplorer2 Resource Report Resource Website 10+ mentions |
CIRCexplorer2 (RRID:SCR_021664) | data processing software, software application, data analysis software, software resource | Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs. | Decipher alternative back splicing, decifer circRNAs splicing pattern, circular RNA analysis, annotate circRNAs | National Natural Science Foundation of China ; Ministry of Science and Technology of China |
PMID:27365365 PMID:30539552 |
Free, Available for download, Freely available | SCR_021664 | 2026-08-14 09:28:22 | 49 | |||||||||
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Bayesian Analysis of Single Cell Sequencing Resource Report Resource Website 1+ mentions |
Bayesian Analysis of Single Cell Sequencing (RRID:SCR_021829) | data processing software, software application, data analysis software, software resource | Software tool for Bayesian analysis of single cell sequencing data. Used to perform statistical analyses of single cell RNA sequencing datasets in context of supervised experiments. | Bayesian analysis, single cell sequencing data, single cell RNA sequencing datasets, statistical analyses, supervised experiments | PMID:26107944 | Free, Available for download, Freely available | https://github.com/catavallejos/BASiCS | SCR_021829 | BASiCS, Bayesian Analysis of Single-Cell Sequencing data | 2026-08-14 09:28:32 | 2 | ||||||||
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Circa Resource Report Resource Website 10+ mentions |
Circa (RRID:SCR_021828) | data processing software, software application, data analytics software, software resource, data visualization software | Software tool used to plot circular plots and visualize genomic data along genomic locations. | OMGenomics, | Restricted | SCR_021828 | visualize genomic data, OMGenomics Circa, circular plots | 2026-08-14 09:28:39 | 19 | ||||||||||
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Biomed Resource Watch Resource Report Resource Website |
Biomed Resource Watch (RRID:SCR_021761) | data or information resource, storage service resource, service resource, data repository | Knowledgebase of biomedical research resources. Repository for storing validation and problematic information about variety of entities within biomedical domain, such as antibodies, cell lines, etc. Enables researchers to submit their own claims about specific entity to make validation/problematic information F.A.I.R. (Findable, Accessable, Interoperable, Reuseable). | FAIR data, biomedical data, data validation, problematic information, problematic cell line, problematic antibody | Free, Available for download, Freely available | SCR_021761 | 2026-08-14 09:28:31 | 0 | |||||||||||
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Rescognito Resource Report Resource Website |
Rescognito (RRID:SCR_021874) | topical portal, portal, web service, data or information resource, data access protocol, software resource | Platform for recognizing and promoting Open Research. Open online service that aims to offer fairer and more democratic platform for recognizing researcher contributions.Allows researchers to openly acknowledge colleagues for meaningful contributions to research process, such as Publication, Mentoring,Teaching,Data sharing,Reproducibility practices, Sharing negative results, Participation in discussion groups,Software development, Clinical trials management, Leadership, Community outreach, Public engagement. ORCID iDs, DOIs, grant IDs and other persistent identifiers are used where available as links to appropriate contributions. | Open Research, Rescognito Inc., platform for recognizing researcher contributions | Free, Freely available | SCR_021874 | 2026-08-14 09:28:40 | 0 | |||||||||||
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SourceMD Resource Report Resource Website |
SourceMD (RRID:SCR_021633) | data or information resource, software resource, data access protocol, web service | Web tool as prototype service to automatically generate Wikidata items using metadata from scholarly publications. Citation lookup tool in Wikipedia platform. Takes persistent identifier for scholarly article and processes it by importing bibliographic metadata into Wikidata items. In August 2018, it was merged with ORCIDator into single tool that allows for fully automated batch processing based on ISBN-13, DOI, ORCID iD, PubMed ID, PMCID identifiers. | Generate Wikidata items, scholarly publications metadata, citation lookup tool, Wikipedia platform, importing bibliographic metadata | is related to: Wikidata | Free, Freely available | https://www.wikidata.org/wiki/Wikidata:SourceMD, https://sourcemd.toolforge.org/, | SCR_021633 | Source M.D., Source Metadata Tool | 2026-08-14 09:28:29 | 0 | ||||||||
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NetMHC Resource Report Resource Website 10+ mentions |
NetMHC (RRID:SCR_021651) | production service resource, web service, data access protocol, software resource, service resource, analysis service resource | Web tool for binding prediction of peptides to MHC class I molecules. The newest version NetMHC- 4.0 is used for prediction of peptide MHC class I binding affinity using gapped sequence alignment that allows insertions and deletions in alignment. | Gapped sequence alignment, peptide-MHC, artificial neural networks, MHC class I system, histocompatibility complex, peptide binding, binding prediction | PMID:18463140 PMID:26515819 |
Free, Freely available | SCR_021651 | NetMHC- 3.0, NetMHC- 2.1, NetMHC- 2.0, NetMHC- 1.0, NetMHC- 3.2, NetMHC- 4.0, NetMHC-3.4 | 2026-08-14 09:28:29 | 39 | |||||||||
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Zeiss LabScope Resource Report Resource Website 1+ mentions |
Zeiss LabScope (RRID:SCR_021768) | data processing software, software application, software resource, image acquisition software, data acquisition software | Software tool for image acquisition using WiFi-enabled Zeiss microscopes. Compatible with Windows PCs and with Apple tablets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Image acquisition, acquisition using WiFi enabled Zeiss microscopes, Zeiss | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_021768 | Zeiss LabScope software | 2026-08-14 09:28:39 | 4 | ||||||||||
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Atherosclerosis Risk in Communities Resource Report Resource Website 10+ mentions |
Atherosclerosis Risk in Communities (RRID:SCR_021769) | ARIC | data or information resource, portal, disease-related portal, topical portal | Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years. | Heart health studies, epidemiologic study, heart disease risk factors, stroke risk factors, cardiovascular and cognitive health connection, atherosclerosis risk | coronary heart disease, stroke, myocardial infarction, atherosclerosis | NHLBI | PMID:2646917 PMID:34112321 |
Free, Freely available | SCR_021769 | The Atherosclerosis Risk in Communities (ARIC) Study | 2026-08-14 09:28:31 | 43 | ||||||
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Papers with Code Resource Report Resource Website 10+ mentions |
Papers with Code (RRID:SCR_021800) | data or information resource, portal, topical portal | Website devoted to papers that contain machine learning datasets, code, methods and evaluation tables. Done together with community, supported by NLP and ML.All content on this website is openly licenced under CC-BY-SA and everyone can contribute.Also operates specialized portals for papers with code in astronomy, physics, computer sciences, mathematics and statistics. | article, machine learning datasets, code, methods, evaluation tables | Free, Freely available | SCR_021800 | 2026-08-14 09:28:39 | 20 | |||||||||||
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IonWizard Resource Report Resource Website 1+ mentions |
IonWizard (RRID:SCR_021764) | data processing software, software application, software resource, data acquisition software | Software tool to perform rapid fluorescence and morphometric real time, synchronous data acquisition with IonOptix systems, as well as polynomial fitting and analysis for myocyte research. Features include data trace averaging and filtering,composite images, and transient analysis. Integrates presentation of fluorescence traces and images, analog voltages, and cell length data under intuitive interface. Analyzes raw data by performing ratio, ion, or linear calibration calculations. | IONOPTIX LLC, polynomial fitting, analysis for myocyte research, data trace averaging and filtering, fluorescence, morphometry | Restricted | SCR_021764 | IonOptix IonWizard | 2026-08-14 09:28:39 | 8 | ||||||||||
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Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data processing software, software application, data analysis software, software resource | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Klarman Cell Observatory ; Manton Foundation ; HHMI ; Ludwig Center at MIT ; Leidos Biomedical Research ; Frederick National Laboratory for Cancer Research ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-08-14 09:28:22 | 3 | |||||||
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FigsharePlus Resource Report Resource Website 1+ mentions |
FigsharePlus (RRID:SCR_021762) | data or information resource, storage service resource, service resource, data repository | Web based interface designed for academic research data management and research data dissemination. Accepts all file types. Enables academics to upload, share, cite and discover all manner of research outputs with security of knowing our hosting options and platform support long term preservation of data.Used to share big datasets from 100GB up. Added features and expert guidance are also included for sharing your data FAIR-ly.During data deposit, personal email support is available and once submitted, Figshare data expert will conduct review of the metadata and spot check of your dataset files and offer guidance, with main aim of enhancing discoverability and reusability. | FAIR data |
is related to: FigShare is related to: NIH Figshare Archive |
https://plus.figshare.com/, https://github.com/figshare/user_documentation | SCR_021762 | 2026-08-14 09:28:24 | 1 | ||||||||||
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TriKinetics DAMSystem3 Software Resource Report Resource Website 1+ mentions |
TriKinetics DAMSystem3 Software (RRID:SCR_021809) | data processing software, software application, software resource, data acquisition software | Software tool for data collection to upload output from set of activity monitors and periodically saves it in disk files on Macintosh or Windows PC. Part of TriKinetics Drosophila Activity Monitoring System. | TriKinetics Inc USA, data collection | is related to: TriKinetics: Drosophila Activity Monitoring System | Free, Freely available, Available for download | https://www.trikinetics.com/Downloads/QuickStart%20Guide.pdf | SCR_021809 | 2026-08-14 09:28:32 | 4 | |||||||||
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PARASAIL Resource Report Resource Website 1+ mentions |
PARASAIL (RRID:SCR_021805) | image analysis software, data processing software, software application, software resource, alignment software | Software tool as multiple sequence alignement for global, local and semi global alignments. | multiple sequence alignement, global alignments, local alignments, semi global alignments, | is listed by: Debian | Pacific Northwest National Laboratory | DOI:10.1186/s12859-016-0930-z | Free, Available for download, Freely available | https://sources.debian.org/src/libparasail-dev/ | SCR_021805 | Pairwise Sequence Alignment Library | 2026-08-14 09:28:25 | 4 | ||||||
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LEON BIS Resource Report Resource Website 1+ mentions |
LEON BIS (RRID:SCR_021803) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool for sequence alignments evaluation. Multiple alignment evaluation of sequence neighbours using Bayesian inference system. Used to distinguish sections in multiple sequence alignments that are conserved across whole family or within subfamilies, and should be useful for automatic, high-throughput genome annotations, 2D/3D structure predictions, protein-protein interaction predictions etc. | sequence alignments evaluation, distinguish sections, multiple sequence alignments, genome annotations, 2D/3D structure predictions, protein-protein interaction predictions | PMID:27387560 | Free, Available for download, Freely available | SCR_021803 | LEON-BIS | 2026-08-14 09:28:39 | 1 | |||||||||
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LINUCS Resource Report Resource Website |
LINUCS (RRID:SCR_001571) | LINUCS | production service resource, data analysis service, software resource, source code, service resource, analysis service resource | Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated | carbohydrate, notation, structure, carbohydrate sequence, canonical description, glycodatabase, glycobioinformatics, algorithm, molecule, sequence |
is related to: sumo is related to: pdb2linucs has parent organization: glycosciences.de |
PMID:11675023 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152883 | SCR_001571 | LINUCS: LInear Notation for Unique description of Carbohydrate Sequences, LInear Notation for Unique description of Carbohydrate Sequences | 2026-08-14 09:24:20 | 0 | ||||||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | database, production service resource, data analysis service, data or information resource, service resource, analysis service resource | A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. | chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Canadian Biotechnology Strategy ; National Research Council Genomics and Health Initiative |
PMID:15289485 | Free, Freely available | biotools:cpndb, OMICS_01511, nif-0000-02694 | https://bio.tools/cpndb | http://www.cpndb.ca/cpnDB/home.php | SCR_002263 | 2026-08-14 09:24:28 | 4 | ||||
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TrainingSpace Resource Report Resource Website 1+ mentions |
TrainingSpace (RRID:SCR_022036) | data or information resource, training resource, portal, online course | Portal that provides multimedia educational content from courses, conference lectures, and laboratory exercises from some of leading neuroscience institutes and societies to be more accessible to global neuroscience community. | Training materials resource, neuroscience multimedia educational content, neuroscience community | Free, Freely available | SCR_022036 | 2026-08-14 09:28:27 | 1 |
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