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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nFuse Resource Report Resource Website 1+ mentions |
nFuse (RRID:SCR_000066) | nFuse | software resource | Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS). | cancer, genomics |
is listed by: OMICtools is listed by: Google Code has parent organization: Simon Fraser University; British Columbia; Canada |
Cancer | PMID:22745232 | Free, Available for download, Freely available, | OMICS_01353 | SCR_000066 | nFuse: Discovery of Complex Genomic Rearrangements in Cancer | 2026-02-14 01:59:36 | 2 | |||||
|
FACS Resource Report Resource Website 1+ mentions |
FACS (RRID:SCR_000055) | FACS | software resource | Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence. | unix/linux, sequence, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SciLifeLab |
PMID:20472541 | Free, Available for download, Freely available | OMICS_02147, biotools:facs | https://bio.tools/facs | SCR_000055 | Fast and Accurate Classification of Sequences | 2026-02-14 01:59:36 | 5 | |||||
|
Batman-Seq Resource Report Resource Website |
Batman-Seq (RRID:SCR_000048) | Batman-Seq | software resource | A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment. | c++ | is hosted by: SourceForge | Free, Available for download, Freely available | OMICS_00651 | SCR_000048 | Basic Alignment Tool for MAny Nucleotides | 2026-02-14 01:59:35 | 0 | |||||||
|
PSGInfer Resource Report Resource Website |
PSGInfer (RRID:SCR_000243) | PSGInfer | software resource | Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. | alternative splicing, rna-seq, probabilistic splice graph |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23846746 | Free, Available for download, Freely available | OMICS_01967 | SCR_000243 | PSGInfer: Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs | 2026-02-14 01:59:39 | 0 | ||||||
|
Cascleave Resource Report Resource Website |
Cascleave (RRID:SCR_000197) | Cascleave | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates. | matlab |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:24149049 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01670 | SCR_000197 | Cascleave 2.0 - Caspase substrate cleavage site prediction, Cascleave 2.0 | 2026-02-14 01:59:39 | 0 | ||||||
|
HEM Resource Report Resource Website |
HEM (RRID:SCR_000194) | HEM | software resource | Software package that fits heterogeneous error models for analysis of microarray data | differential expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Virginia; Virginia; USA |
PMID:15044230 | Free, Available for download, Freely available | OMICS_01970 | SCR_000194 | HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions | 2026-02-14 01:59:38 | 0 | ||||||
|
Molegro Virtual Docker Resource Report Resource Website 1+ mentions |
Molegro Virtual Docker (RRID:SCR_000190) | Molegro Virtual Docker | software resource | An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets. | protein ligand, protein target, visualization, integrated platform | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01603 | SCR_000190 | 2026-02-14 01:59:38 | 9 | ||||||||
|
Zhejiang University; Zhejiang; China Resource Report Resource Website 1+ mentions |
Zhejiang University; Zhejiang; China (RRID:SCR_000224) | ZJU | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A public research university with twelve main academic disciplines that include science, engineering, agriculture and medicine. The university has campuses across China in locations such as Yuquan, Zhijiang and Zhoushan. It has studies available in undergraduate, graduate and post-doctorate degrees. | china, undergraduate, graduate, post doctorate, research university |
uses: ReadCube is parent organization of: DaTo is parent organization of: PlantNATsDB - Plant Natural Antisense Transcripts DataBase |
THIS RESOURCE IS NO LONGER IN SERVICE | grid.13402.34, Wikidata:Q197543, Crossref funder ID:501100004835, nlx_149178, ISNI:0000 0004 1759 700X | https://ror.org/00a2xv884 | SCR_000224 | Zhejiang University | 2026-02-14 01:59:39 | 1 | ||||||
|
MRNet Resource Report Resource Website 1+ mentions |
MRNet (RRID:SCR_000225) | MRNet | software resource | A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication. | is listed by: OMICtools | DOI:10.1145/1048935.1050172 | Free, Available for download, Freely available | OMICS_01686 | SCR_000225 | MRNet: A Multicast/Reduction Network | 2026-02-14 01:59:39 | 1 | |||||||
|
FastQ Screen Resource Report Resource Website 10+ mentions |
FastQ Screen (RRID:SCR_000141) | FastQ Screen | software resource | Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. | perl, FASEB list |
is listed by: OMICtools has parent organization: Babraham Institute |
PMID:30254741 | Free, Available for download, Freely available | OMICS_01042 | SCR_000141 | 2026-02-14 01:59:38 | 48 | |||||||
|
Trinity College Dublin; Dublin; Ireland Resource Report Resource Website 1+ mentions |
Trinity College Dublin; Dublin; Ireland (RRID:SCR_000261) | TCD | university | A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level. | arts, humanities, social sciences, mathematics, engineering, health sciences, Dublin, Ireland |
is related to: Pharma-Planta Consortium is related to: Biomedical Diagnostics Institute is parent organization of: ExplorEnz is parent organization of: CASBAH is parent organization of: Trinity Biobank is parent organization of: Random.org |
nlx_87233 | SCR_000261 | College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin, Trinity, Trinity College Dublin, Trinity College, Trinity College Dublin - University of Dublin, University of Dublin | 2026-02-14 01:59:41 | 1 | ||||||||
|
University of Florida; Florida; USA Resource Report Resource Website 1+ mentions |
University of Florida; Florida; USA (RRID:SCR_000145) | UF | university | Public research university in Gainesville, Florida, United States. Member of state university system of Florida with undergraduate and graduate programs in arts and sciences. | university, undergraduate, graduate, florida |
is listed by: Florida ExpertNet is affiliated with: Helmsley Cellular Research Hub is related to: Clinical and Translational Science Awards Consortium is related to: EnCor Biotechnology Inc. is related to: National High Magnetic Field Laboratory High B/T Core Facility is related to: National High Magnetic Field Laboratory Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility is related to: National High Magnetic Field Laboratory Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility is related to: Mnemiopsis Genome Project Portal is parent organization of: University of Florida College of Medicine; Florida; USA is parent organization of: ESPRIT is parent organization of: University of FLorida College of Medicine Molecular Pathology Core Facility is parent organization of: SNPper is parent organization of: ShapeComplexAtlas is parent organization of: University of Florida Labs and Facilities is parent organization of: MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation is parent organization of: SobekCM is parent organization of: M-pick is parent organization of: ESPRIT-Tree is parent organization of: VIVO is parent organization of: MRM NeAt (Neurological Atlas) Mouse Brain Database is parent organization of: PASTA is parent organization of: Multi-fiber Reconstruction from DW-MRI is parent organization of: fanDTasia Java Applet: DT-MRI Processing is parent organization of: Mouse Brain Image Visualizer (MBIV) is parent organization of: Barth Syndrome Biorepository is parent organization of: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 is parent organization of: International Affective Picture System is parent organization of: FastqSifter is parent organization of: University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility is parent organization of: University of Florida ICBR Cytometry Core Facility is parent organization of: University of Florida ICBR Bioinformatics Core Facility is parent organization of: University of Florida ICBR Electron Microscopy Core Facility is parent organization of: University of Florida ICBR Monoclonal Antibody Core Facility is parent organization of: University of Florida ICBR Gene Expression and Genotyping Core Facility is parent organization of: University of Florida ICBR NextGen DNA Sequencing Core Facility is parent organization of: University of Florida ICBR Proteomics and Mass Spectrometry Core Facility is parent organization of: Human Atlas of Neonatal Development and Early Life Immunity is parent organization of: Florida research open source synchronization tool is parent organization of: University of Florida UF Scripps Biomedical Research Bioinformatics and Statistics Core Facility is parent organization of: University of Florida Scripps Florida Histology Core Facility is parent organization of: University of Florida Health Mass Spectrometry and Proteomics Core Facility is parent organization of: University of Florida Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core Facility is parent organization of: University of Florida Systems Physiology and Omics Core Facility is parent organization of: University of FLorida College of Medicine Molecular Pathology Core Facility is parent organization of: University of Florida Herbert Wertheim College of Engineering Research Service Centers Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Mouse Behavior Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genetic Perturbation Screening Core Facility is parent organization of: University of Florida Scripps Institute for Biomedical Innovation and Technology Flow Cytometry Core Facility is parent organization of: University of Florida Scripps Institute for Biomedical Innovation and Technology Metabolic Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genomics Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Advanced Light Microscopy Core Facility hosts: National High Magnetic Field Laboratory |
ISNI:0000 0004 1936 8091, nlx_80063, Crossref funder ID:100007698, Wikidata:Q501758, grid.15276.37 | https://ror.org/02y3ad647 | SCR_000145 | University of Florida (UF), University of Florida, UFlorida | 2026-02-14 01:59:37 | 1 | |||||||
|
MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | Mass Spectrometry Analysis Software | 2026-02-14 01:59:40 | 1 | ||||||||
|
GEOquery Resource Report Resource Website 10+ mentions |
GEOquery (RRID:SCR_000146) | GEOquery | software resource | Software that establishes a bridge between GEO and BioConductor. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: GEO2R has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:17496320 | Free, Available for download, Freely available | biotools:geoquery, OMICS_01972 | https://bio.tools/geoquery https://sources.debian.org/src/r-bioc-geoquery/ |
SCR_000146 | GEOquery - Get data from NCBI Gene Expression Omnibus (GEO) | 2026-02-14 01:59:37 | 18 | |||||
|
Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina Resource Report Resource Website |
Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina (RRID:SCR_000264) | School of Medical Sciences - UCA | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. Private medical school in Buenos Aires that offers degree programs in the medical sciences. Resource is in Spanish. | buenos aires, medicine, graduate, private, medical school |
has parent organization: Pontifical Catholic University of Argentina; Buenos Aires; Argentina is parent organization of: Biomedical Research Program UCA |
THIS RESOURCE IS NO LONGER IN SERVICE. | https://ror.org/0422kzb24 | http://www.uca.edu.ar/index.php/home/index/es/universidad/facultades/buenos-aires/cs-medicas | SCR_000264 | UCA School of Medical Sciences, UCA Facultad de Ciencias M�dicas, Pontificia Universidad Cat�lica Argentina Facultad de Ciencias M�dicas, Pontifical Catholic University of Argentina School of Medical Sciences | 2026-02-14 01:59:40 | 0 | ||||||
|
Polish Ministry of Science and Higher Education Resource Report Resource Website 1+ mentions |
Polish Ministry of Science and Higher Education (RRID:SCR_000251) | institution | Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research. | funding, government, agency, higher education, scientific research, public, poland | ISNI: 0000 0001 0684 6072, Wikidata: Q4294468, grid.425823.a, Crossref funder ID: 501100004569, nlx_149369 | https://ror.org/05dwvd537 | http://www.nauka.gov.pl/en/ | SCR_000251 | Ministry of Science and Higher Education - Republic of Poland, Polish Ministry of Science Higher Education, Ministry of Science and Higher Education (Poland) | 2026-02-14 01:59:40 | 9 | ||||||||
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Polytechnic University of Catalonia; Barcelona; Spain Resource Report Resource Website 1+ mentions |
Polytechnic University of Catalonia; Barcelona; Spain (RRID:SCR_000252) | UPC | university | A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER). | public, architecture, engineering, technology, catalan, internationalization, architecture | is parent organization of: TaxoAssignement | nlx_158613 | SCR_000252 | Universitat Politècnica de Catalunya, Universitat Politècnica de Catalunya BarcelonaTech, UPC BarcelonaTech, Universitat Politecnica de Catalunya, Universitat Politecnica de Catalunya BarcelonaTech, BarcelonaTech, Polytechnic University of Catalonia | 2026-02-14 01:59:40 | 1 | ||||||||
|
Polytechnic University of Valencia; Valencia; Spain Resource Report Resource Website |
Polytechnic University of Valencia; Valencia; Spain (RRID:SCR_000255) | UPV | university | A technical university in Spain which offers degree programs in 14 different faculties, including business administration, computer science and industrial engineering at the undergraduate, graduate and postdoctoral level. The school has five different campuses. | technical, polytechnic, business administration, computer science, architecture, industrial engineering, design, cartography, fine arts, management | is parent organization of: DTI denoising | nlx_157969 | SCR_000255 | Polytechnic University of Valencia, Technical University of Valencia, Universidad Politécnica de Valencia, Universitat Politecnica de Valencia, Universitat Politècnica de València | 2026-02-14 01:59:41 | 0 | ||||||||
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Pompeu Fabra University; Barcelona; Spain Resource Report Resource Website |
Pompeu Fabra University; Barcelona; Spain (RRID:SCR_000256) | UPF | university | Public university in Spain that offers programs in social sciences and humanities, health and life sciences, international training in communication and communication sciences. Has colleges based on topics such as law, translation and interpretation, and engineering. Research is organized into economics and business, experimental sciences and health, law. | University, public, Spain, Barcelona |
is related to: EMIF is related to: Centre for Genomic Regulation; Barcelona; Spain is parent organization of: EEG time series Data Sets is parent organization of: Bern-Barcelona EEG database is parent organization of: Reliable detection of directional couplings using rank statistics is parent organization of: Characterizing unidirectional couplings between point processes and flows is parent organization of: Detecting event-related time-dependent directional couplings is parent organization of: Nonlinear time series analysis in a nutshell is parent organization of: Time-resolved and time-scale adaptive measures of spike train synchrony is parent organization of: Gene-Disease Association Type Ontology is parent organization of: DisGeNET is parent organization of: aneurIST is parent organization of: Functional Coverage of the Proteome is parent organization of: Cellular Biology of Addiction is parent organization of: GIMIAS is parent organization of: TransFIC is parent organization of: BioMoby |
Wikidata:Q24543, nlx_52215, grid.5612.0, ISNI:0000 0001 2172 2676 | https://ror.org/04n0g0b29 | SCR_000256 | Universitat Pompeu Fabra, Pompeu Fabra University, UPF Barcelona | 2026-02-14 01:59:40 | 0 | |||||||
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Sorbonne University; Paris; France Resource Report Resource Website |
Sorbonne University; Paris; France (RRID:SCR_000246) | UPMC | university | A public research university in France that emphasizes medical and scientific research centered on four themes: life and health, the living earth and environment, matter and new materials and modeling and engineering. It is a member of the Sorbonne Universities alliance. | public, engineering, modeling, environment, france, public research university, living earth |
is related to: EMIF is parent organization of: Parseq is parent organization of: Cordelier Research Center is parent organization of: XNBC |
, Wikidata: Q41497113, GRID: grid.462844.8, Crossref Funder ID: 501100019125, ISNI: 0000 0001 2308 1657, nlx_17035 | https://ror.org/02en5vm52 | SCR_000246 | , University Pierre and Marie Curie, Pierre and Marie Curie University, University Pierre et Marie Curie, Sorbonne Université; Pierre and Marie Curie University, Paris; Universite Pierre et Marie Curie | 2026-02-14 01:59:39 | 0 |
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