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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SleepTrip Resource Report Resource Website 10+ mentions |
SleepTrip (RRID:SCR_017318) | data processing software, software application, data analysis software, software resource | Software as branch of FieldTrip with added functionality for sleep analyses, like calculating sleep tables, descriptives, ploting hypnograms, detecting slow waves, sleep spindles, REMS and their cooccurrence etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | slow, wave, oscillation, spindle, cooccurrence, rapid, eye, movements, sleep table, hypnogram |
is related to: SpiSOP works with: FieldTrip |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/Frederik-D-Weber/sleeptrip | SCR_017318 | SpiSOP | 2026-08-14 09:27:35 | 16 | ||||||||
|
GraphClust2 Resource Report Resource Website 1+ mentions |
GraphClust2 (RRID:SCR_017286) | data processing software, web application, software application, data analysis software, software resource | Software tool for scalable clustering of RNAs based on sequence and secondary structures similarities. Implemented within Galaxy framework. Used for studying RNA function. | scalable, clustering, RNA, sequence, secondary, structure, function, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
German Research Foundation Collaborative Research Centre 992 Medical Epigenetics ; German Federal Ministry of Education and Research |
PMID:31808801 PMID:22689765 |
Free, Available for download, Freely available | biotools:GraphClust2 | https://bio.tools/GraphClust2 | SCR_017286 | GraphClust, GraphClust-2 | 2026-08-14 09:27:35 | 4 | |||||
|
redbiom Resource Report Resource Website 1+ mentions |
redbiom (RRID:SCR_017285) | production service resource, data processing software, data analysis service, software application, data analysis software, software resource, service resource, analysis service resource | Software tool for allowing samples that contain microbiome features to be rapidly identified. Rapid sample discovery and feature characterization system. Integrated with existing analysis tools to enable fast, large scale microbiome searches and discovery of new microbiome relationships. Service for sample metadata and sample data. | microbiome, feature, identify, characterize, analysis, metadata, sample, data | PMID:31239397 | Free, Available for download, Freely available | SCR_017285 | 2026-08-14 09:27:44 | 5 | ||||||||||
|
PILER Resource Report Resource Website 10+ mentions |
PILER (RRID:SCR_017333) | data processing software, software application, data analysis software, software resource | Software tool for analyzing repetitive DNA found in genome sequences. Software package for identification and classification of genomic repeats. Used for identifying patterns of local alignments induced by certain classes of repeats. | analysis, repetitive, DNA, genome, sequence, classification, alignment | is listed by: OMICtools | PMID:15961452 | Free, Available for download, Freely available | https://omictools.com/piler-tool | SCR_017333 | 2026-08-14 09:27:36 | 15 | ||||||||
|
Bonsai Resource Report Resource Website 100+ mentions |
Bonsai (RRID:SCR_017218) | data processing software, software application, software resource, data acquisition software | Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world. | Event, based, framework, processing, controlling, data, stream | European Union Seventh Framework Programme ; Bial Foundation ; Foundation for Science and Technology ; Champalimaud Foundation |
PMID:25904861 | Free, Available for download, Freely available | https://github.com/bonsai-rx/bonsai-rx.github.io | SCR_017218 | 2026-08-14 09:28:00 | 105 | ||||||||
|
RNAstructure Resource Report Resource Website 50+ mentions |
RNAstructure (RRID:SCR_017216) | simulation software, production service resource, web service, data access protocol, software application, software resource, service resource, analysis service resource | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | 2026-08-14 09:27:43 | 58 | ||||||||
|
Excel Statistics Resource Report Resource Website 10+ mentions |
Excel Statistics (RRID:SCR_017294) | software toolkit, software application, data analytics software, software resource | Software tool for statistical analysis by BellCurve that adds statistical analysis methods to Excel menu . | statistical, analysis, BellCurve, Excell | Restricted | SCR_017294 | 2026-08-14 09:28:02 | 29 | |||||||||||
|
SerialEM Resource Report Resource Website 100+ mentions |
SerialEM (RRID:SCR_017293) | data processing software, software application, software resource, data acquisition software | Software tool for automated EM data acquisition. Used for efficient tilt series acquisition and interface for image capture, display, and storage and for control of some aspects of microscope function. | automated, data, acquisition, tilt, image, capture, display, storage, microscope | NCRR RR00592; NIGMS P01 GM61306 |
PMID:16182563 | Restricted | SCR_017293 | 2026-08-14 09:27:35 | 228 | |||||||||
|
PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | data processing software, software application, data analysis software, software resource | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-08-14 09:27:43 | 19 | ||||||
|
TWOSEX-MSChart Resource Report Resource Website 10+ mentions |
TWOSEX-MSChart (RRID:SCR_017298) | data processing software, software application, data analysis software, software resource | Software tool used to conduct life table analysis focused on development of cohort or population for animal species with two sexes. Parent organization is National Chung Hsing University, Taichung, Taiwan. | life, table, analysis, development, cohort, population, animal, species, sex | Restricted | SCR_017298 | 2026-08-14 09:28:02 | 14 | |||||||||||
|
Proovread Resource Report Resource Website 10+ mentions |
Proovread (RRID:SCR_017331) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool for PacBio hybrid error correction through iterative short read consensus. | PacBio, hybrid, error, correction, short, read, consensus, DNA, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: BWA is related to: BLASR is related to: SHRiMP |
European Research Council | PMID:25015988 | Free, Available for download, Freely available | biotools:proovread | https://bio.tools/proovread | SCR_017331 | 2026-08-14 09:28:03 | 14 | ||||||
|
SynGO Resource Report Resource Website 100+ mentions |
SynGO (RRID:SCR_017330) | production service resource, data analysis service, controlled vocabulary, ontology, data or information resource, service resource, analysis service resource | Evidence based, expert curated knowledge base for synapse. Universal reference for synapse research and online analysis platform for interpretation of omics data. Interactive knowledge base that accumulates available research about synapse biology using Gene Ontology annotations to novel ontology terms. | Synapse, evidence, curated, base, reference, analysis, omics, data, ontology, gene, annotation | uses: Gene Ontology | Stanley Center for Psychiatric Research at The Broad Institute of MIT and Harvard ; European Union ; CERCA Program/Generalitat de Catalunya ; NINDS NS36251; German Federal Ministry of Education and Research |
PMID:31171447 | Free, Freely available | SCR_017330 | Synaptic Gene Ontologies | 2026-08-14 09:27:36 | 187 | |||||||
|
Protomo Resource Report Resource Website 1+ mentions |
Protomo (RRID:SCR_017296) | data processing software, software application, image processing software, software resource | Software tool for electron tomography and 3D image processing. Software package used in electron tomography for marker free alignment and 3D reconstruction of tilt series. Tomography software package distributed for linux operating system and developed by Hanspeter Winkler. | electron, tomography, 3D, image, processing | NIGMS GM30598; NIGMS GM64346 |
PMID:16973379 | Restricted | SCR_017296 | 2026-08-14 09:27:35 | 5 | |||||||||
|
TOMO3D Resource Report Resource Website 1+ mentions |
TOMO3D (RRID:SCR_017295) | image analysis software, data processing software, software application, software resource, image reconstruction software | Software tool for fast tomographic reconstruction on multicore computers. Used for electron tomography studies with increasing resolution needs. | tomographic, reconstruction, multicore, computer, electron, resoulion | ERDF | PMID:25528570 | Restricted | SCR_017295 | 2026-08-14 09:27:44 | 6 | |||||||||
|
Phangorn Resource Report Resource Website 10+ mentions |
Phangorn (RRID:SCR_017302) | software toolkit, data processing software, software application, data analysis software, software resource, data visualization software | Software R package for phylogenetic reconstruction and analysis. Used for estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, distance methods and Hadamard conjugation. Allows to compare trees, models selection and offers visualizations for trees and split networks. | phylogenetic, tree, network, reconstruction, analysis, estimation, Maximum, Likelihood, Parsimony, distance, method, Hadamard conjugation |
is listed by: Debian is listed by: OMICtools is related to: CRAN |
Muséum National D Histoire Naturelle | DOI:10.1093/bioinformatics/btq706 | Free, Available for download, Freely available | OMICS_12497 | https://github.com/KlausVigo/phangorn, https://sources.debian.org/src/r-cran-phangorn/ | SCR_017302 | Phangorn R package | 2026-08-14 09:28:03 | 28 | |||||
|
SICAS Medical Image Repository Resource Report Resource Website 1+ mentions |
SICAS Medical Image Repository (RRID:SCR_017420) | storage service resource, service resource, data repository | Medical image repository to store medical research data. | Medical, image, repository, store, data |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Free, Freely available | r3d100011560 | https://doi.org/10.17616/R3HP8C | SCR_017420 | Medical Image Repository, SICAS, SICAS Medical Image Repository | 2026-08-14 09:27:46 | 5 | |||||||
|
TempEst Resource Report Resource Website 100+ mentions |
TempEst (RRID:SCR_017304) | software toolkit, data processing software, software application, data analysis software, software resource | Software tool for investigating temporal signal and clocklikeness of molecular phylogenies. Used for visualization and analysis of temporally sampled sequence data to assess whether there is sufficient temporal signal in data to proceed with phylogenetic molecular clock analysis, and to identify sequences whose genetic divergence and sampling date are incongruent. Not available for downloading as of August 8, 2019. | temporal, signal, clocklikeness, molecular, phylogeny, visualization, analysis, temporally, sampled, sequenced, data, identify, genetic, incongruent | is related to: BEAST | EU Seventh Framework Programme ; ERC Grant |
DOI:doi.org/10.1093/ve/vew007 | Restricted | http://tree.bio.ed.ac.uk/software/tempest/ | SCR_017304 | Path-O-Gen, tempest | 2026-08-14 09:27:35 | 166 | ||||||
|
University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility Resource Report Resource Website |
University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility (RRID:SCR_017382) | NMR Facility, UF NMR Facility | access service resource, service resource, degree granting program, postdoctoral program resource, training service resource, training resource, undergraduate program resource, core facility | Facility serves students and faculty of University of Florida, and researchers from industry who use facility instruments to check outcome of reactions or characterize compounds. Instruments include Inova 500 MHz magnet with 2 RF Channels, Inova 500 MHz magnet with 3 RF Channels, Mercury 300 MHz (m4n and m8n), Mercury 300 MHz Broadband, Agilent 600 MHZ Magnet, and several NMR probes. | Laboratory portal, Biochemistry, Chemistry, NMR, NMR instrument, NMR Imaging and Localized Spectroscopy, Nuclear Magnetic Resonance, University of Florida, National High Magnetic Field Laboratory | has parent organization: University of Florida; Florida; USA | Restricted | https://nmr.chem.ufl.edu/trainings/, https://nmr.chem.ufl.edu/safety/, https://nmr.chem.ufl.edu/nmr-policies/, | SCR_017382 | UF Department of Chemistry NMR Facility | 2026-08-14 09:28:05 | 0 | |||||||
|
brainGraph Resource Report Resource Website 10+ mentions |
brainGraph (RRID:SCR_017260) | data processing software, software application, data analysis software, software resource | Software R package for performing graph theory analyses of brain MRI data. | graph, theory, analysis, brain, MRI, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CRAN |
Free, Available for download, Freely available | https://www.nitrc.org/projects/braingraph/, https://rdrr.io/cran/brainGraph/, https://www.r-pkg.org/pkg/brainGraph | SCR_017260 | brainGraph - Graph Theory Analysis of Brain MRI Data in R, brainGraph | 2026-08-14 09:27:35 | 16 | ||||||||
|
Morpheus by Broad Institute Resource Report Resource Website 1000+ mentions |
Morpheus by Broad Institute (RRID:SCR_017386) | data processing software, software application, data analysis software, software resource, data visualization software, service resource | Software tool for versatile matrix visualization and analysis. Program to generate heatmaps from input data. JavaScript matrix visualization and analysis. | Matrix, visualization, analysis, heatmap, input, data, Java | has parent organization: Broad Institute | Free, Available for download, Freely available | https://github.com/cmap/morpheus.js | SCR_017386 | 2026-08-14 09:27:45 | 2141 |
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