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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | software resource, data processing software, software application, data analysis software | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-08-05 10:46:49 | 2 | ||||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | data or information resource, portal, consortium, disease-related portal, topical portal, organization portal | 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 | 2026-08-05 10:46:43 | 131 | |||||||||
|
IQ-TREE Resource Report Resource Website 500+ mentions |
IQ-TREE (RRID:SCR_017254) | software resource, data processing software, software application, data analysis software | Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference. | stochastic, algorithm, estimate, maximum, likelihood, phylogeny, phylogenomic, inference, data, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Vienna; Vienna; Austria |
Austrian Science Fund ; University of Vienna |
PMID:25371430 | Free, Available for download, Freely available | biotools:ufboot2 | https://bio.tools/ufboot2/ | SCR_017254 | 2026-08-05 10:46:45 | 790 | ||||||
|
proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | software resource, data processing software, software application, data analysis software | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIA R01 AG046170; NIAID U19 AI118610 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | probabilisticMulti Omics DataMatcher | 2026-08-05 10:46:49 | 1 | |||||||
|
miRTarVisPlus Resource Report Resource Website 1+ mentions |
miRTarVisPlus (RRID:SCR_017103) | miRTarVis+ | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis 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 | 2026-08-05 10:46:50 | 3 | |||||
|
seqNMF Resource Report Resource Website 1+ mentions |
seqNMF (RRID:SCR_017068) | software resource, data processing software, software application, 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 | 2026-08-05 10:46:49 | 5 | ||||||||
|
University of Gothenburg Bioinformatics Core Facility Resource Report Resource Website |
University of Gothenburg Bioinformatics Core Facility (RRID:SCR_017189) | GU Bioinformatics Core Facility | core facility, access service resource, data analysis service, production service resource, service resource, analysis 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 | 2026-08-05 10:46:44 | 0 | ||||||||
|
iMicrobe Resource Report Resource Website 10+ mentions |
iMicrobe (RRID:SCR_017108) | organism-related portal, data or information resource, topical portal, portal | 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 | 2026-08-05 10:46:43 | 19 | |||||||||
|
Ponemah Resource Report Resource Website 10+ mentions |
Ponemah (RRID:SCR_017107) | data processing software, data acquisition software, software application, data analysis software, software resource | 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 | 2026-08-05 10:46:48 | 20 | |||||||||||
|
Juicer Resource Report Resource Website 100+ mentions |
Juicer (RRID:SCR_017226) | software resource, data processing software, software application, data analysis software | Software platform for analyzing kilobase resolution Hi-C data. Open source tool for analyzing terabase scale Hi-C datasets. Allowes to transform raw sequence data into normalized contact maps. | analysis, kilobase, resolution, Hi-C, data, terabase, dataset, transform, raw, sequence, normalized, contact, map | has parent organization: Baylor College of Medicine; Houston; Texas | NIH Office of the Director DP2 OD008540; NHLBI U01 HL130010; NSF PHY-1427654; NHGRI HG006193; Welch Foundation ; Cancer Prevention Research Institute of Texas ; NVIDIA Research Center Award ; IBM University Challenge Award ; Google Research Award ; McNair Medical Institute Scholar Award ; President Early Career Award in Science and Engineering ; NHGRI HG003067; PD Soros Fellowship |
PMID:27467249 | Free, Available for download, Freely available | SCR_017226 | 2026-08-05 10:46:52 | 108 | ||||||||
|
ot-tools Resource Report Resource Website 1+ mentions |
ot-tools (RRID:SCR_017191) | software resource, data processing software, software application, 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 | 2026-08-05 10:46:48 | 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 or information resource, core facility, training service resource, access service resource, data analysis service, production service resource, service resource, analysis service 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 | 2026-08-05 10:46:51 | 0 | ||||||||||
|
Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | data or information resource, data repository, service resource, storage 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 | 2026-08-05 10:46:43 | 14 | |||||||
|
BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis 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 | 2026-08-05 10:46:48 | 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 or information resource, core facility, training service resource, access service resource, software resource, data analysis service, production service resource, service resource, analysis service 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 | 2026-08-05 10:46:49 | 0 | ||||||||
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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 | core facility, access service resource, software resource, data analysis service, production service resource, service resource, analysis 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 | 2026-08-05 10:46:51 | 0 | |||||||||
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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 | core facility, training service resource, access service resource, data analysis service, production service resource, service resource, analysis 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 | 2026-08-05 10:46:44 | 0 | ||||||||
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shovill Resource Report Resource Website 100+ mentions |
shovill (RRID:SCR_017077) | data processing software, software application, sequence analysis software, data analysis software, software resource | 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 | 2026-08-05 10:46:49 | 445 | ||||||||
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cwl-metrics Resource Report Resource Website 1+ mentions |
cwl-metrics (RRID:SCR_017076) | CWL-metrics | software toolkit, software library, software resource | 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 | 2026-08-05 10:46:42 | 1 | |||||
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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, data or information resource, service resource, core facility | 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 | 2026-08-05 10:46:51 | 9 |
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