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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | web service, storage service resource, software resource, data access protocol, data repository, service resource, data or information resource | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NIGMS R01 GM103551; NIGMS R01 GM121696; NHGRI U54 HG008097; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | 2026-08-04 09:44:07 | 0 | ||||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | portal, topical portal, disease-related portal, consortium, organization portal, data or information resource | Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. | identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility | has parent organization: National Cancer Institute | cancer | SCR_017135 | Clinical Proteomic Tumor Analysis Consortium | 2026-08-04 09:44:05 | 131 | |||||||||
|
miRTarVisPlus Resource Report Resource Website 1+ mentions |
miRTarVisPlus (RRID:SCR_017103) | miRTarVis+ | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web based interactive visual analytics tool for miRNA target predictions and integrative analyses of multiple prediction results. Used for sequence based miRNA target prediction by exploiting miRNA-mRNA expression profile data. | interactive, visual, analytical, miRNA, target, prediction, analysis, mRNA, expression, data | has parent organization: Seoul National University; Seoul; South Korea | National Research Foundation of Korea ; Hankuk University of Foreign Studies Research Fund |
PMID:28600227 | Free, Freely available | http://hcil.snu.ac.kr/research/mirtarvisplus | SCR_017103 | mirtarvisplus | 2026-08-04 09:44:05 | 3 | |||||
|
tidyr Resource Report Resource Website 50+ mentions |
tidyr (RRID:SCR_017102) | software application, software resource, data management software | Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data. | tidy, data, spread, gather, function |
is used by: PlotsOfData is used by: tidyverse is listed by: CRAN is related to: R Project for Statistical Computing works with: dplyr |
Free, Available for download, Freely available | https://github.com/tidyverse/tidyr, https://tidyr.tidyverse.org/ | SCR_017102 | 2026-08-04 09:44:06 | 62 | |||||||||
|
seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | data processing software, software application, software resource, data analysis software | Software tool for unsupervised discovery of sequential structure. Used to detect sequences in neural data generated by internal behaviors, such as animal thinking or sleeping. Used for unsupervised discovery of temporal sequences in high dimensional datasets in neuroscience without reference to external markers. | sequence, structure, high, dimention, dataset, neuroscience, repeated, sequential, pattern, data | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | Simons Foundation Simons Collaboration for the Global Brain ; NIDCD R01 DC009183; G Harold and Leila Y. Mathers Foundation ; U.S. Department of Defense NDSEG Fellowship program ; Department of Energy ; Labor and Economic Growth Computational Science Graduate Fellowship ; NIBIB T32 EB019940; NINDS U19 NS10 4648; NIMH R25 MH062204 |
PMID:30719973 | Free, Available for download, Freely available | SCR_017068 | 2026-08-04 09:44:03 | 5 | ||||||||
|
University of Gothenburg Bioinformatics Core Facility Resource Report Resource Website |
University of Gothenburg Bioinformatics Core Facility (RRID:SCR_017189) | GU Bioinformatics Core Facility | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource | Core assists with statistical and bioinformatics consultation and data analysis. | bioinformatics, data, analysis, consulting, statistical | has parent organization: University of Gothenburg; Gothenburg; Sweden | Open | SCR_017189 | University of Gothenburg, GU, Bioinformatics Core Facility | 2026-08-04 09:44:06 | 0 | ||||||||
|
iMicrobe Resource Report Resource Website 10+ mentions |
iMicrobe (RRID:SCR_017108) | topical portal, portal, organism-related portal, data or information resource | Portal to provide integrated and federated system that interconnects diverse microbiome data sets, bioinformatics tools, and community resources. Built on guiding principles for FAIR data. Open source, community driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with broader community. Partners with CyVerse and XSEDE. | microbiome, dataset, exchange, discovery, data | has parent organization: University of Arizona; Arizona; USA | NSF ; Gordon and Betty Moore Fundation |
Free, Freely available | SCR_017108 | 2026-08-04 09:44:05 | 19 | |||||||||
|
Ponemah Resource Report Resource Website 10+ mentions |
Ponemah (RRID:SCR_017107) | data processing software, data analysis software, software resource, software application, data acquisition software | Software tool for complete physiologic data acquisition and analysis used by physiologists, pharmacologists, and toxicologists to collect, analyze, and summarize preclinical study data. Allows to custom design configuration based on needs, budget and convenience without need for any programming. | Data Sciences International, Inc., physiologic, data, acquisition, analysis, collect, summerize, preclinical, custom, design | Available for purchase | SCR_017107 | 2026-08-04 09:44:06 | 20 | |||||||||||
|
CDC Diseases & Conditions Resource Report Resource Website 1+ mentions |
CDC Diseases & Conditions (RRID:SCR_017070) | data or information resource, controlled vocabulary | List of diseases and conditions on Centers for Disease Control and Prevention website., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | vocabulary, list, data, condition, center, disease, control, prevention | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017070 | 2026-08-04 09:44:04 | 3 | |||||||||||
|
ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | data processing software, software application, software resource, data analysis software | Software tools for analysis of cellular cryo-ET data. | analysis, cellular, cryo-ET, data | Free, Available for download, Freely available | SCR_017191 | 2026-08-04 09:44:06 | 5 | |||||||||||
|
Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility Resource Report Resource Website |
Gulbenkian Institute of Science Bioinformatics and Computational Unit Core Facility (RRID:SCR_017190) | data analysis service, analysis service resource, access service resource, training service resource, core facility, production service resource, service resource, data or information resource | IGC Core in Oeiras, Portugal, promotes use of computational methods in biological research, through training and development of resources and materials, supports biological data analysis using computational methods, conducts research and development in bioinformatics, in particular in data flows, data warehousing and data analyses. | bioinformatics, consulting, data, analysis, management, repository | Open | SCR_017190 | Bioinformatics and Computational Unit, IGC, core facility, Instituto Gulbenkian de Ciencia, Gulbenkian Institute of Science | 2026-08-04 09:44:08 | 0 | ||||||||||
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Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | storage service resource, data repository, data or information resource, service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-08-04 09:44:05 | 14 | |||||||
|
BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs. | quantitative, trait, loci, mapping, bulk, segregant, analysis, yeast, sequencing, data, processing, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Luxembourg; Luxembourg; Luxembourg |
Fonds Nationale de la Recherche (FNR) Luxembourg | Free, Freely available, Registration required | biotools:BSA4Yeast | https://bio.tools/BSA4Yeast | SCR_017113 | Bulk Segregant Analysis for Yeast | 2026-08-04 09:44:06 | 1 | ||||||
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University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility Resource Report Resource Website |
University of Edinburgh College of Medicine and Veterinary Medicine MRC Institute of Genetics and Molecular Medicine Bioinformatics Analysis Core Facility (RRID:SCR_017194) | MRC Institute of Genetics and Molecular Medicine BAC | data analysis service, analysis service resource, access service resource, software resource, training service resource, core facility, production service resource, service resource, data or information resource | Core provides advice, training, provision of computational tools and collaborative expertise to all IGMM researchers. | bioinformatics, data, analysis, sequencing | has parent organization: University of Edinburgh; Scotland; United Kingdom | Restricted | SCR_017194 | The University of Edinburgh, Bioinformatics Analysis, College of Medicine and Veterinary Medicine, College of Medicine & Veterinary Medicine, Core Facility, Institute of Genetics and Molecular Medicine, IGMM, MRC | 2026-08-04 09:44:06 | 0 | ||||||||
|
Genome Institute of Singapore Scientific and Research Computing Core Facility Resource Report Resource Website |
Genome Institute of Singapore Scientific and Research Computing Core Facility (RRID:SCR_017193) | GIS Scientific and Research Computing | data analysis service, analysis service resource, access service resource, software resource, core facility, production service resource, service resource | Core provides research computing resources including bioinformatics, application development, data management and IT infrastructure to support next generation sequencing technologies, human genotyping, high throughput screening and computational biology researchers. | bioinformatics, genomic, data, management, next, generation, sequencing, genotyping, analysis | Open | SCR_017193 | Core Facility, GIS, Scientific & Research Computing, Scientific and Research Computing, Genome Institute of Singapore | 2026-08-04 09:44:08 | 0 | |||||||||
|
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) | CTR Bioinformatics Core Facility | data analysis service, analysis service resource, access service resource, training service resource, core facility, production service resource, service resource | Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training. | bioinformatics, sequencing, RNA, genome, methylation, protein, alignment, data, image, analysis | has parent organization: University of Cambridge; Cambridge; United Kingdom | Restricted | SCR_017192 | Center for Trophoblast Research, Centre for Trophoblast Research, Bioinformatics Core Facility, University of Cambridge | 2026-08-04 09:44:06 | 0 | ||||||||
|
shovill Resource Report Resource Website 100+ mentions |
shovill (RRID:SCR_017077) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit. | assembly, bacteria, isolate, genome, Illumina, paired, end, read, data, haploid, organism, bio.tools |
uses: SPAdes is listed by: Debian is listed by: bio.tools is related to: Trimmomatic is related to: SAMTOOLS is related to: BWA is related to: FLASH is related to: Velvet is related to: Pilon |
Free, Available for download, Freely available | , biotools:shovill, BioTools:shovill | https://bio.tools/shovill, https://sources.debian.org/src/shovill/ | SCR_017077 | 2026-08-04 09:44:04 | 445 | ||||||||
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cwl-metrics Resource Report Resource Website 1+ mentions |
cwl-metrics (RRID:SCR_017076) | CWL-metrics | software toolkit, software resource, software library | Software framework to collect and analyze computational resource usage of workflow runs based on common workflow language CWL. Used to share set of tools packaged in containers. Enables users to choose proper cloud instance for workflow runs based on run time metrics data. Operating system Unix/Linux. | collect, analyze, computational, resource, usage, workflow, common, language, container, cloud, data, analysis | is listed by: OMICtools | Japan Science and Technology Agency | DOI:10.1101/456756 | Free, Available for download, Freely available | OMICS_32746 | SCR_017076 | Common Workflow Language-metrics, common workflow language metrix | 2026-08-04 09:44:05 | 1 | |||||
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UMI-tools Resource Report Resource Website 100+ mentions |
UMI-tools (RRID:SCR_017048) | data processing software, software application, software resource, data analysis software | Open source software package for handling Unique Molecular Identifiers in NGS data sets. | unique, molecular, identifier, NGS, data, dataset, random, oligonucleotide, barcode, sequencing, copy, molecule, PCR, amplification, bio.tools |
is listed by: Debian is listed by: bio.tools |
Medical Research Council | PMID:28100584 | Free, Available for download, Freely available | biotools:umi-tools | https://bio.tools/umi-tools | SCR_017048 | Unique Molecular Identifiers tools | 2026-08-04 09:44:05 | 126 | |||||
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University of Malaga Andalusian Platform of Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
University of Malaga Andalusian Platform of Bioinformatics Core Facility (RRID:SCR_017169) | SCBI, scbi | access service resource, core facility, data or information resource, service resource | Provides assistance in computing, nanotechnology, and biological fields. Provides scientific support and resources to the UMA research groups, public institutions and private companies. | bioinformatics, computing, nanotechnology, biology, data | has parent organization: University of Malaga; Andalusia; Spain | Open | SCR_017169 | Universidad de Malaga, scbi, UMA, Plataforma Andaluza de Bioinformatica, University of Malaga, SCBI, Supercomputing and Bioinnovation Center | 2026-08-04 09:44:06 | 9 |
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