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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 | 2026-09-03 04:43:08 | 2 | |||||
|
GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, data processing software, software application, software resource | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
ADVANCE Program at Brown University ; Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | Geometric Analysis of Structural Variants | 2026-09-03 04:43:08 | 4 | ||||
|
ChIPmeta Resource Report Resource Website |
ChIPmeta (RRID:SCR_000054) | data analysis software, data processing software, software application, software resource | Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets. | chip-chip, chip-seq, ChIP-chip and ChIP-seq datasets analysis, | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02172 | SCR_000054 | ChIPmeta with HHM | 2026-09-03 04:43:06 | 0 | ||||||||
|
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 | 2026-09-03 04:43:07 | 6 | |||||
|
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 | 2026-09-03 04:43:06 | 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 | 2026-09-03 04:43:24 | 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 | 2026-09-03 04:43:21 | 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 | 2026-09-03 04:43:21 | 0 | ||||||
|
AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | consortium, data or information resource, organization portal, portal | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | 2026-09-03 04:43:24 | 3 | |||||||
|
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 | 2026-09-03 04:43:20 | 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 | 2026-09-03 04:43:23 | 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 | 2026-09-03 04:43:24 | 1 | |||||||
|
FastQ Screen Resource Report Resource Website 50+ 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 | 2026-09-03 04:43:16 | 50 | |||||||
|
RSEM Resource Report Resource Website 100+ mentions |
RSEM (RRID:SCR_000262) | data analysis software, data processing software, software application, software resource | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-09-03 04:43:26 | 115 | ||||||
|
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 | 2026-09-03 04:43:26 | 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: 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 is parent organization of: National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility is parent organization of: University of Florida Nanoscale Research Facility NRF 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 | 2026-09-03 04:43:17 | 1 | |||||||
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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 | 2026-09-03 04:43:26 | 2 | ||||||||
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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) | 2026-09-03 04:43:16 | 20 | |||||
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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 | 2026-09-03 04:43:28 | 0 | ||||||
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M(at)CBETH Resource Report Resource Website |
M(at)CBETH (RRID:SCR_000265) | M(at)CBETH | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset. | microarray, classification, performing microarray classification, |
is listed by: OMICtools has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium |
PMID:15890742 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02292 | SCR_000265 | MicroArray Classification BEnchmarking Tool on Host server | 2026-09-03 04:43:26 | 0 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
