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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | SciCrunch Registry | 2026-10-10 12:35:45 | 4 | ||||||||
|
Academy Biomedical Company Resource Report Resource Website |
Academy Biomedical Company (RRID:SCR_001108) | commercial organization | Commercial antibody supply company that focuses on providing antibodies for research in cardiovascular and atherosclerosis. | antibody, cardiovascular, athersclerosis, antibody supplier | nlx_152249 | SCR_001108 | SciCrunch Registry | Academy Bio-Medical Company, Academy Biomedical Company Inc. | 2026-10-10 12:35:54 | 0 | ||||||||||
|
RmiR Resource Report Resource Website |
RmiR (RRID:SCR_001069) | RmiR | data analysis software, data processing software, sequence analysis software, software application, software resource | R package that contains functions to merge microRNA and respective targets using different databases. | micro rna, mrna, function, target, r, sequence analysis software |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00789 | https://rdrr.io/bioc/RmiR/ | SCR_001069 | SciCrunch Registry | 2026-10-10 12:35:51 | 0 | |||||||
|
BreakFusion Resource Report Resource Website 1+ mentions |
BreakFusion (RRID:SCR_001102) | BreakFusion | software resource | Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data. | computational pipeline, gene fusions, rna, sequence, data, perl, c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:22563071 DOI:10.1093/bioinformatics/bts272 |
Free, Available for download, Freely available | OMICS_01342 | SCR_001102 | SciCrunch Registry | 2026-10-10 12:35:47 | 3 | |||||||
|
Virginia Commonwealth University School of Medicine; Virginia; USA Resource Report Resource Website |
Virginia Commonwealth University School of Medicine; Virginia; USA (RRID:SCR_001061) | VCU SOM | university | Medical school division of Virginia Commonwealth University. | virginia, medical, medicine, commonwealth, medical school, continuing medical education, residency | has parent organization: Virginia Commonwealth University; Virginia; USA | nlx_64661 | SCR_001061 | SciCrunch Registry | VCU School of Medicine | 2026-10-10 12:35:45 | 0 | ||||||||
|
U.S. Department of Education Resource Report Resource Website 1+ mentions |
U.S. Department of Education (RRID:SCR_001060) | ED | institution | The United States federal government Department of Education, which oversees policies on federal financial aid for education, collecting data and disseminating research, and working to promote key educational discussions and equal access to education. | education, federal, financial aid, fafsa, government department | is parent organization of: National Institute on Disability and Rehabilitation Research | Available to groups within the United States of America | grid.419881.d, Crossref funder ID: 100000138, Wikidata: Q861556, ISNI: 0000 0001 2176 2483, nlx_143871 | https://ror.org/021adze67 | SCR_001060 | SciCrunch Registry | ED.gov, United States Department of Education | 2026-10-10 12:35:52 | 2 | ||||||
|
NPEBseq Resource Report Resource Website 1+ mentions |
NPEBseq (RRID:SCR_001014) | NPEBseq | software resource | A method for non-parametric, empirical Bayesian-based analysis of RNA-seq count data. | rna, rna sequence, seq, empirical, Bayesian, nonparametric | is listed by: OMICtools | PMID:23981227 | OMICS_01312 | http://bioinformatics.wistar.upenn.edu/NPEBseq | SCR_001014 | SciCrunch Registry | 2026-10-10 12:35:45 | 1 | |||||||
|
SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | SciCrunch Registry | 2026-10-10 12:35:51 | 1 | ||||||
|
Hytest Resource Report Resource Website 1+ mentions |
Hytest (RRID:SCR_001133) | commercial organization | A commercial antibody supplier that specializes in high-quality monoclonal antibodies and antigens for the diagnostic industry. | antibody, monoclonal, antigen, diagnostic, research and development, r and d | nlx_152378, grid.417767.4, Wikidata: Q5952196 | https://ror.org/031cpdm45 | SCR_001133 | SciCrunch Registry | HyTest Ltd. | 2026-10-10 12:35:48 | 5 | |||||||||
|
ASC Resource Report Resource Website 1+ mentions |
ASC (RRID:SCR_001013) | ASC | software resource | Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available. | sample variation, rna, dna, biology, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brown University; Rhode Island; USA |
biotools:sqn, OMICS_01298 | https://bio.tools/sqn | SCR_001013 | SciCrunch Registry | 2026-10-10 12:35:44 | 1 | ||||||||
|
BioLegend Resource Report Resource Website 5000+ mentions |
BioLegend (RRID:SCR_001134) | commercial organization | Commercial antibody supplier and developer for biomedical research. These products are compatible with use in flow cytometry and mass cytometry, immunoprecipitation and chip, western blotting, immunofluorescence microscopy, and quantitative multiplexing. | commercial, antibody, reagent, biomedical, research, san diego | nlx_152302 | SCR_001134 | SciCrunch Registry | 2026-10-10 12:35:53 | 6621 | |||||||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data analysis software, data processing software, sequence analysis software, software application, software resource | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | SciCrunch Registry | 2026-10-10 12:35:52 | 0 | |||||||||
|
GDC Resource Report Resource Website 1+ mentions |
GDC (RRID:SCR_001007) | GDC | data analysis software, data management software, data processing software, software application, software resource | A C++ application designed for compression of genome collections from the same species. | compression, genome collection, c++, genome, software |
is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/srep11565 | Source code available for download | OMICS_00958 | https://github.com/refresh-bio/GDC2 | SCR_001007 | SciCrunch Registry | GDC 2, Genome Differential Compressor, Genome Differential Compressor (GDC) | 2026-10-10 12:35:45 | 1 | |||||
|
NewEast Biosciences Resource Report Resource Website |
NewEast Biosciences (RRID:SCR_001129) | commercial organization | Commercial supplier which provides antibodies, assay kits, biomarkers, and proteins. | antibody, pennsylvania, commercial, assay kit, oncogene | nlx_152421 | SCR_001129 | SciCrunch Registry | 2026-10-10 12:35:53 | 0 | |||||||||||
|
AutoAssemblyD Resource Report Resource Website |
AutoAssemblyD (RRID:SCR_001087) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers. | genome, genome assembly, xml, sequence analysis software, local genome assembly, remote genome assembly, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24143057 | Free, Available for download, Freely available | biotools:autoassemblyd, OMICS_00874 | https://bio.tools/autoassemblyd | SCR_001087 | SciCrunch Registry | 2026-10-10 12:35:45 | 0 | |||||||
|
Kyoto Encyclopedia of Genes and Genomes Expression Database Resource Report Resource Website 1000+ mentions |
Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) | KEGG Expression Database | data or information resource, data repository, database, service resource, storage service resource | Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community. | encyclopedia, endogenous, environment, enzyme, escherichia coli, exogenous, expression, family, functional, gene, genetic, anabaena, bacillus subtilis, biological system, biology, building block, cell, cellular, chemical, community, complex, genome, genomic, hierarchy, interaction, japanese, mapping, metabolic, metabolic pathway databases, microarray, molecular, molecular wiring, nomenclature, order, organism, ortholog, pathway, process, protein, reaction, research, sequence, specie, substance, synechocystis, FASEB list |
is listed by: LabWorm is affiliated with: KEGG has parent organization: Kyoto University; Kyoto; Japan |
PMID:9847135 PMID:10592173 |
Free, Available for download, Freely available | r3d100011570, nif-0000-21234 | https://doi.org/10.17616/R3792T | SCR_001120 | SciCrunch Registry | Kyoto Encyclopedia of Genes and Genomes Expression Database | 2026-10-10 12:35:46 | 1279 | |||||
|
Howard University; Washington D.C. Resource Report Resource Website |
Howard University; Washington D.C. (RRID:SCR_001084) | HU | university | A federally chartered, private, coeducational, nonsectarian, historically black university in Washington, D.C. Howard University has graduate schools in many fields, including business, nursing, engineering, and medicine. | undergraduate, graduate, master's, doctoral, phD, institution, university, nonsectarian |
is related to: Clinical and Translational Science Awards Consortium is parent organization of: Howard Flow Cytometry Core is parent organization of: Howard Imaging Core Facility: Molecular Imaging Laboratory is parent organization of: Howard Biobehavioral Core Laboratory is parent organization of: Howard Biostatistics Core is parent organization of: Howard University Center for Computational Biology and Bioinformatics Core Facility is parent organization of: Howard Molecular Genetics Core is parent organization of: Howard Nanoscale Science and Engineering Facility is parent organization of: Howard RCMI Proteomics Facility |
nlx_152178 | SCR_001084 | SciCrunch Registry | Howard, Howard University, Howard U | 2026-10-10 12:35:52 | 0 | ||||||||
|
University of Florida College of Medicine Neuroscience Resource Report Resource Website |
University of Florida College of Medicine Neuroscience (RRID:SCR_001081) | data or information resource, department portal, organization portal, portal | A department at the University of Florida's College of Medicine that offers programs of study on neural function and how it changes with injury and disease. The institution's research ranges from fundamental discovery to clinical application. These neuroscience programs are offered at the undergraduate, graduate, postdoctoral and resident level. | neuroscience, neural function, undergraduate, graduate, postdoctoral, resident, clinical, injury, disease | nif-0000-02172 | SCR_001081 | SciCrunch Registry | UFL | 2026-10-10 12:35:45 | 0 | ||||||||||
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jmzML Resource Report Resource Website 1+ mentions |
jmzML (RRID:SCR_001119) | software resource | A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard. | standalone software, mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:20127693 | Free, Available for download, Freely available | biotools:jmzml, OMICS_03340 | https://bio.tools/jmzml | SCR_001119 | SciCrunch Registry | 2026-10-10 12:35:54 | 1 | |||||||
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CISCRP- The Center for Information and Study on Clinical Research Participation Resource Report Resource Website |
CISCRP- The Center for Information and Study on Clinical Research Participation (RRID:SCR_001152) | data or information resource, portal, topical portal | CISCRP is a resource for information on participation in, understanding of, and resources for clinical research participants and scientists. The mission of the Center is to educate, inform and empower patients, the public, medical and research professionals, the media and policymakers about clinical research participation and what it means to be an active participant in the clinical research process, promote greater awareness and understanding of clinical research participation and the role that it plays in public health, facilitate more effective collaboration among all members of the clinical research enterprise, and provide resources for the research community to better understand the study volunteer. To that end, the Center has developed a broad national awareness and education initiative in order to better inform the public at large about clinical study information. Furthermore, on its website, the Center offers program and event information related to clinical trials, an information center with facts, figures, informational resources, and FAQs for both patients and researchers, and a mailing list of clinical trial information. :The Center also maintains its own search engine website, : :searchclinicaltrials.org : : :, for those looking for further clinical trial information. The Center for Information and Study on Clinical Research Participation is located in Dedham, MA. :NIF thanks the : :Parkinson's Disease Foundation : : :for their referral of this resource to us. | clinical research, clinical study | nif-0000-11642 | SCR_001152 | SciCrunch Registry | CISCRP | 2026-10-10 12:35:48 | 0 |
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