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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TNO-DECO Resource Report Resource Website |
TNO-DECO (RRID:SCR_000440) | software resource | Matlab code for preprocessing gas chromatography mass spectrometry data. | matlab, mass spectrometry | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02660 | SCR_000440 | SciCrunch Registry | 2026-10-17 01:24:41 | 0 | |||||||||
|
MiRdup Resource Report Resource Website 1+ mentions |
MiRdup (RRID:SCR_000316) | software resource | A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA. | pre-miRNA, miRNA, mRNA, splicing, predictions |
is listed by: OMICtools has parent organization: McGill University; Montreal; Canada |
PMID:23748953 | Free, Available for download, Freely available | OMICS_00404 | https://www.cs.mcgill.ca/~blanchem/mirdup/ | http://This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. | SCR_000316 | SciCrunch Registry | 2026-10-17 01:24:36 | 1 | ||||||
|
WILEY Interdisciplinary Reviews Resource Report Resource Website |
WILEY Interdisciplinary Reviews (RRID:SCR_000392) | WIREs | data or information resource, portal, topical portal | Wiley Interdisciplinary Reviews series combines features of encyclopedic reference works and review journals in innovative online format. They are designed to promote cross-disciplinary research ethos while maintaining the highest scientific and presentational standards, but should be viewed first and foremost as evolving online databases of cutting-edge reviews. | encyclopedic reference works, review journals, databases of reviews, | nif-0000-10668 | http://www.wiley.com/WileyCDA/Section/id-370078.html | SCR_000392 | SciCrunch Registry | Wiley Interdisciplinary Reviews series | 2026-10-17 01:24:42 | 0 | ||||||||
|
Time Event Ontology Resource Report Resource Website |
Time Event Ontology (RRID:SCR_000310) | TEO | controlled vocabulary, data or information resource, ontology | Ontology for representing events, time, and their relationships. | owl | is listed by: BioPortal | nlx_157610 | SCR_000310 | SciCrunch Registry | 2026-10-17 01:24:37 | 0 | |||||||||
|
Variation Ontology Resource Report Resource Website |
Variation Ontology (RRID:SCR_000311) | VARIO | controlled vocabulary, data or information resource, ontology | An ontology for standardized, systematic description of effects, consequences and mechanisms of variations. | obo | is listed by: BioPortal | nlx_157622 | SCR_000311 | SciCrunch Registry | 2026-10-17 01:24:40 | 0 | |||||||||
|
RStudio Resource Report Resource Website 1000+ mentions |
RStudio (RRID:SCR_000432) | RStudio | software resource | Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux). | R, statistical, computing, environment |
is used by: PlotsOfData is listed by: Debian is listed by: SoftCite is related to: rSPRITE is related to: shinyCircoss is parent organization of: Shiny is required by: circlncRNAnet |
Restricted | SciRes_000113 | https://sources.debian.org/src/rstudio/, https://posit.co/download/rstudio-desktop/ | http://www.rstudio.com/ | SCR_000432 | SciCrunch Registry | 2026-10-17 01:24:40 | 1191 | ||||||
|
Semantic DICOM Ontology Resource Report Resource Website |
Semantic DICOM Ontology (RRID:SCR_000309) | SEDI | controlled vocabulary, data or information resource, ontology | An ontology for DICOM as used in the SeDI project. | owl | is listed by: BioPortal | nlx_157583 | SCR_000309 | SciCrunch Registry | 2026-10-17 01:24:40 | 0 | |||||||||
|
QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | SciCrunch Registry | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-10-17 01:24:41 | 0 | |||||||
|
Scribe Resource Report Resource Website |
Scribe (RRID:SCR_000423) | Scribe | software resource | Scribe encodes papers to populate the BrainMap Database | magnetic resonance, pet, spect |
is used by: brainmap.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Freely available | nlx_155958 | SCR_000423 | SciCrunch Registry | 2026-10-17 01:24:41 | 0 | ||||||||
|
pFind Studio: pLink Resource Report Resource Website 10+ mentions |
pFind Studio: pLink (RRID:SCR_000084) | pLink | software resource | Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mass spectrometry, proteomics, pFind Studio, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:22772728 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02404, biotools:pLink-2 | https://github.com/pFindStudio/pLink3/releases | http://pfind.ict.ac.cn/software/pLink/index.html | SCR_000084 | SciCrunch Registry | , pLink, pLink (pFind Studio), pLink2 | 2026-10-17 01:24:32 | 15 | ||||
|
Spotfinder Resource Report Resource Website 1+ mentions |
Spotfinder (RRID:SCR_000085) | Spotfinder | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression. | c++ |
is listed by: OMICtools has parent organization: Dana-Farber Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00848 | SCR_000085 | SciCrunch Registry | TIGR Spotfinder | 2026-10-17 01:24:33 | 8 | |||||||
|
Faceted Search Based Ontology Visualizer Resource Report Resource Website |
Faceted Search Based Ontology Visualizer (RRID:SCR_000124) | ontologyviz | software resource | Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy. | computational neuroscience, magnetic resonance, ontology, functional neuroanatomy, facet, visualization | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | nlx_155874 | SCR_000124 | SciCrunch Registry | 2026-10-17 01:24:36 | 0 | ||||||||
|
GOALIE Resource Report Resource Website |
GOALIE (RRID:SCR_000088) | GOALIE | software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database. Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene ontology, statistical analysis, time-course |
is listed by: Gene Ontology Tools has parent organization: NYU Bioinformatics Group |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149255 | SCR_000088 | SciCrunch Registry | Generalized Ontological Algorithmic Logical Invariants Extractor, Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) | 2026-10-17 01:24:32 | 0 | |||||||
|
Parallel-META Resource Report Resource Website 1+ mentions |
Parallel-META (RRID:SCR_000121) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis. | data mining, microbial community data, comparative taxonomics, metagenomic analysis, parallel algorithms | is listed by: OMICtools | PMID:23046922 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01519 | SCR_000121 | SciCrunch Registry | Parallel META, Parallel Meta | 2026-10-17 01:24:33 | 4 | |||||||
|
Adaptively Sampled Particle Fluids Resource Report Resource Website |
Adaptively Sampled Particle Fluids (RRID:SCR_000083) | ASPF | simulation software, software application, software resource, source code | Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux. | fluid simulation, lagrangian particle fluid, linux |
is listed by: Biositemaps is listed by: Simtk.org |
Free, Available for download, Freely available | nif-0000-23328 | SCR_000083 | SciCrunch Registry | 2026-10-17 01:24:34 | 0 | ||||||||
|
BioLemmatizer Resource Report Resource Website 1+ mentions |
BioLemmatizer (RRID:SCR_000117) | software resource | A domain-specific lemmatization software tool for the morphological analysis of biomedical literature. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22464129 | Free, Available for download, Freely available | OMICS_04827 | https://sourceforge.net/projects/biolemmatizer/ | SCR_000117 | SciCrunch Registry | 2026-10-17 01:24:32 | 2 | |||||||
|
Orphelia Resource Report Resource Website 1+ mentions |
Orphelia (RRID:SCR_000119) | simulation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment. | metagenomic open reading frame, tool, resource, protein, genes, DNA, phyologenetic origin, machine learning, linear discriminates, artificial neural network, computation, scientific computing, fragment | is listed by: OMICtools | PMID:19429689 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01492 | SCR_000119 | SciCrunch Registry | 2026-10-17 01:24:33 | 2 | ||||||||
|
ReQON Resource Report Resource Website |
ReQON (RRID:SCR_000075) | ReQON | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format. | preprocessing, quality control, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:22946927 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02033 | SCR_000075 | SciCrunch Registry | Recalibrating Quality Of Nucleotides | 2026-10-17 01:24:33 | 0 | ||||||
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QuadGT Resource Report Resource Website 1+ mentions |
QuadGT (RRID:SCR_000073) | QuadGT | software resource | Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples. | single-nucleotide variant, sequenced genome, genotype, genome |
is listed by: OMICtools has parent organization: University of Montreal; Quebec; Canada |
Normal, Tumor, Cancer | Canada National Sciences and Engineering Research Council ; Canadian Institutes for Health Research ; Terry Fox Research Institute |
PMID:23734724 | Free, Available for download, Freely available | OMICS_02108 | SCR_000073 | SciCrunch Registry | 2026-10-17 01:24:32 | 1 | |||||
|
Google Sites Resource Report Resource Website 1+ mentions |
Google Sites (RRID:SCR_000112) | Sites | service resource | A free online service to easily create and share webpages. | website, sharing, authoring tool |
is parent organization of: PELICAN is parent organization of: dbNSFP |
Free | nlx_157257 | SCR_000112 | SciCrunch Registry | 2026-10-17 01:24:35 | 2 |
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