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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ClustVis Resource Report Resource Website 500+ mentions Issue |
ClustVis (RRID:SCR_017133) | data analysis service, analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web user interface for visualizing clustering of multivariate data. Web server allows users to upload their own data and create Principal Component Analysis plots and heatmaps. | visualizing, clustering, multivariate, data, principal, component, analysis, plot, heatmap, bio.tools |
uses: Shiny uses: ggplot2 uses: pheatmap uses: RColorBrewer uses: FactoMineR is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: University of Tartu; Tartu; Estonia |
Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Federation of Pharmaceutical Industries and Associations ; European Regional Development Fund ; Estonian Research Council ; European Commission ; EFPIA |
PMID:25969447 | biotools:clustvis, OMICS_08539 | https://github.com/taunometsalu/ClustVis, https://bio.tools/clustvis | SCR_017133 | 2026-08-04 09:44:05 | 798 | |||||||
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University of North Carolina Charlotte Bioinformatics Services Division Resource Report Resource Website |
University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) | BiSD, UNC Charlotte BiSD | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource, data or information resource | Core to assist with analyzing and interpreting data produced by genomic technologies. | bioinformatics, analysis, data, genomic | Open | SCR_017182 | , Charlotte, University of North Carolina, BiSD, Bioinformatics Services Division, UNC | 2026-08-04 09:44:06 | 0 | |||||||||
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GAGE Resource Report Resource Website 50+ mentions |
GAGE (RRID:SCR_017067) | data processing software, software application, software resource, data analysis software | Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies. | gene, set, enrichment, pathway, batch, comparison, parallel, analysis, heterogeneous, data |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_017067 | Generally Applicable Gene-set Enrichment for pathway analysis, gage, Generally Applicable Gene-set Enrichment, GSEA | 2026-08-04 09:44:04 | 50 | |||||||||
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City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) | IGBC | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource, data or information resource | Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators. | bioinformatics, genomic, data, analysis, service, next, sequencing | Restricted | SCR_017188 | , City of Hope, Integrative Genomics and Bioinformatics Core, Bioinformatics Core Facility, National Medical Center, IGBC | 2026-08-04 09:44:06 | 1 | |||||||||
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Harvard School of Public Health Microbiome Analysis Core Facility Resource Report Resource Website |
Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) | HSPH Microbiome Analysis Core | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource, data or information resource | Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations. | bioinformatics, consulting, microbiome, omic, data, analysis | has parent organization: Harvard University; Cambridge; United States | Open | SCR_017187 | , HSPH, Harvard School of Public Health, Microbiome Analysis, facility, Core | 2026-08-04 09:44:08 | 0 | ||||||||
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Source code for analysis of GC-MS data - Rice HxD Project Resource Report Resource Website 1+ mentions |
Source code for analysis of GC-MS data - Rice HxD Project (RRID:SCR_017073) | data processing software, source code, data analysis software, software resource, software application, data visualization software | Source code used in the analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice exposed to combined drought and heat stress. | analysis, GC-MS, data, rice, sample, statistics, workflow | Free, Available for download, Freely available | SCR_017073 | 2026-08-04 09:44:05 | 1 | |||||||||||
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University of Cambridge Department of Plant Sciences Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) | University of Cambridge Bioinformatics Core Facility | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource | Core provides assistance in data analysis to support members of Plant Sciences. | bioinformatics, data, analysis, service | has parent organization: University of Cambridge; Cambridge; United Kingdom | SCR_017164 | Department of Plant Sciences, Core Facility, Bioinformatics, University of Cambridge | 2026-08-04 09:44:05 | 0 | |||||||||
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UCSF Gladstone Institutes Bioinformatics Core Facility Resource Report Resource Website |
UCSF Gladstone Institutes Bioinformatics Core Facility (RRID:SCR_017178) | UCSF Gladstone Institutes Bioinformatics Core | 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 consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools. | Bioinformatics, consulting, data, analysis, sequencing, RNA-seq, DNA-seq, ChIP-seq, ATAC-seq, statistics, variant, calling, normalization | Open | SCR_017178 | Bioinformatics Core, Gladstone Core Services, University California San Fransisco, UCSF, Gladstone Institutes | 2026-08-04 09:44:06 | 0 | |||||||||
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University of Manchester Bioinformatics Core Facility Resource Report Resource Website 1+ mentions |
University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) | Manchester Bioinformatics Facility | data analysis service, analysis service resource, access service resource, software resource, core facility, production service resource, service resource | Core provides assistance in integrative analysis of genomic datasets to support faculty. | bioinformatics, analysis, genomic, data, dataset | has parent organization: University of Manchester; Manchester; United Kingdom | Restricted | SCR_017171 | , Bioinformatics Facility, University of Manchester, Bioinformatics Core Facility | 2026-08-04 09:44:07 | 2 | ||||||||
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Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility Resource Report Resource Website |
Vall dHebron Institut de Recerca Statistics and Bioinformatics Unit Core Facility (RRID:SCR_017175) | UEB | 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 at Vall dHebron Institut de Recerca, Barcelona, Spain to provide data analysis, softwares and training programs in statistics and bioinformatics for clinical research at VHIR. | bioinformatics, next, generation, sequencing, data, analysis, DNA, RNA, omics, microarray, RTqPCR, metagenomics, methylation | Restricted | SCR_017175 | , Barcelona, Vall dHebron Institut de Recerca, Support Unit in Methodology for Biomedical Research, UEB, Statistics and Bioinformatics Unit, USMIB | 2026-08-04 09:44:06 | 0 | |||||||||
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Duke University Omics Data Analysis Core Facility Resource Report Resource Website |
Duke University Omics Data Analysis Core Facility (RRID:SCR_017174) | data analysis service, analysis service resource, access service resource, training service resource, core facility, production service resource, service resource, data or information resource | Genomic Analysis and Bioinformatics core for data analysis associated with performing complex and data intensive projects in life science research of Duke University and Duke Medical School. Provides expertise, training, data analysis in next generation sequencing, array and proteomic based technologies. | bioinformatics, data, analysis, training, expertise, next, generation, sequencing, array, proteomic, omics | has parent organization: Duke University; North Carolina; USA | Restricted | SCR_017174 | Analysis Core, Resource, Core Facility, Genomic Analysis and Bioinformatics, Duke University, Omics Data | 2026-08-04 09:44:08 | 0 | |||||||||
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BinPacker Resource Report Resource Website 10+ mentions |
BinPacker (RRID:SCR_017038) | data processing software, software application, software resource, data analysis software | Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. | de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; NSF 1553680; NCRR P20 RR01 6460; NIGMS P20 GM103429 |
PMID:26894997 | Free, Available for download, Freely available | OMICS_11199, biotools:binpacker | http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download, http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download, https://bio.tools/binpacker | SCR_017038 | 2026-08-04 09:44:03 | 10 | ||||||
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Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility Resource Report Resource Website |
Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) | BCF | data analysis service, analysis service resource, access service resource, core facility, production service resource, service resource, database, data or information resource | Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services. | metagenomics, proteomics, protein, structure, functional, genomics, programming, scripting, data | Restricted | SCR_017152 | BCF, Core Facility, University of Oslo, Rikshospitalet-Radiumhospitalet, Bioinformatics | 2026-08-04 09:44:06 | 0 | |||||||||
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CentroidFold Resource Report Resource Website 10+ mentions |
CentroidFold (RRID:SCR_017253) | simulation software, web service, software resource, data access protocol, software application | Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator. | RNA, secondary, structure, prediction, centroid, estimator, sequecne, data, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
New Energy and Industrial Technology Development Organization of Japan ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; Internal fund of Computational Biology Research Center |
PMID:19435882 | Free, Freely available | biotools:centroidfold, OMICS_03449 | https://bio.tools/centroidfold | SCR_017253 | 2026-08-04 09:44:09 | 15 | ||||||
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CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | data processing software, software application, software resource, data analysis software | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-08-04 09:44:06 | 489 | |||||||||
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3D de novo assembly Resource Report Resource Website 10+ mentions |
3D de novo assembly (RRID:SCR_017227) | data processing software, software application, software resource, data analysis software | Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly. | de novo, assembly, 3D, DNA, HI-C, data, scaffold, pipeline, chromosome, genome | DOI:10.1126/science.aal3327 | Free, Available for download, Freely available | SCR_017227 | 2026-08-04 09:44:07 | 40 | ||||||||||
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | data analysis service, portal, analysis service resource, expression atlas, storage service resource, software resource, consortium, controlled vocabulary, application programming interface, data access protocol, organization portal, production service resource, service resource, data repository, ontology, atlas, database, data or information resource | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | NIDA U54 DA036134; NCI R01 CA163849; NIGMS R25 GM056929; NCATS UH3 TR000906; NCI U19 CA179512; NIDDK P30 DK63720; NHLBI K23 HL127099; NHLBI R01 HL136685; NIA R01 AG059729; NCATS UH3 TR000943; NCI R35 CA209904; NCI CA217685; NHLBI R01 HL122547; American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch |
PMID:30951672 | Restricted | SCR_017221 | 2026-08-04 09:44:09 | 24 | |||||||
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Connectome Computation System Resource Report Resource Website 10+ mentions |
Connectome Computation System (RRID:SCR_017342) | CCS | data processing software, software application, software resource, data analysis software | Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies. | Multimodal, human, brain, imaging, data, analysis, connectome, magnetic, resonance | DOI:10.1007/s11434-014-0698-3 | Free, Available for download, Freely available | SCR_017342 | 2026-08-04 09:44:09 | 15 | |||||||||
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miRpathDB Resource Report Resource Website 50+ mentions |
miRpathDB (RRID:SCR_017356) | web service, software resource, data access protocol, database, data or information resource | Collection of single miRNAs that regulate pathways, gene ontologies and other categories, hence complementing available miRNA target enrichment programs, tailored for miRNA sets. New dictionary on microRNAs and target pathways. Database to augment available target pathway web-servers by providing researches access to information which pathways are regulated by miRNA, which miRNAs target pathway and how specific regulations are. | Collection, miRNA, data, pathway, gene, ontology, dataset, dictionary, target, regulation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Saarland University ; Germany |
PMID:27742822 | biotools:miRPathDb | https://bio.tools/miRPathDB | SCR_017356 | miRNA Pathway Dictionary Database | 2026-08-04 09:44:09 | 52 | ||||||
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Computational Suite for Bioinformaticians and Biologists Resource Report Resource Website 1+ mentions |
Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) | CSBB | data processing software, software application, software resource, data analysis software | Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments. | analysis, sequencing, data, command, line, expression, normalization, convert | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_17554 | https://github.com/csbbcompbio | SCR_017234 | CSBB-v3.0, CSBB-v1.0, CSBB-v2.0, Computational Suite for Bioinformaticians and Biologists | 2026-08-04 09:44:09 | 6 |
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