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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-07-25 12:05:32 | 0 | |||||||
|
PAPi Resource Report Resource Website 50+ mentions |
PAPi (RRID:SCR_002857) | software resource | An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20929912 | Free, Freely available, Available for download | OMICS_02653 | SCR_002857 | PAPi - Predict metabolic pathway activity based on metabolomics data, Pathway Activity Profiling | 2026-07-25 12:05:32 | 53 | |||||||
|
National Academies Press Resource Report Resource Website 10+ mentions |
National Academies Press (RRID:SCR_002844) | institution | The National Academies Press (NAP) was created by the National Academies to publish the reports issued by the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council, all operating under a charter granted by the Congress of the United States. The NAP publishes more than 200 books a year on a wide range of topics in science, engineering, and health, capturing the most authoritative views on important issues in science and health policy. The institutions represented by the NAP are unique in that they attract the nation's leading experts in every field to serve on their award-winning panels and committees. This is the right place for definitive information on everything from space science to animal nutrition. Many books can be read on-line for free. NAP also offers many titles in electronic Adobe PDF format. Hundreds of these books can be downloaded for free by the chapter or the entire book, while others are available for purchase. Sponsors: This resource is supported by The National Academies. | engineering, academy, animal, medicine, national, nutrition, research, science | Free, Freely available | ISNI: 0000 0004 0466 615X, Wikidata: Q6970107, grid.431670.7, nif-0000-25219 | https://ror.org/02a6ztn45 | SCR_002844 | NAP | 2026-07-25 12:05:35 | 40 | ||||||||
|
University of Coimbra; Coimbra; Portugal Resource Report Resource Website |
University of Coimbra; Coimbra; Portugal (RRID:SCR_002842) | UC | university | Public university in Coimbra, Portugal that offers degree programs in a variety of fields including law, medicine, science and technology, pharmaceuticals, and sports sciences. | public university, portugal, degree program |
is parent organization of: EPILAB is parent organization of: University of Coimbra ViralVector Core Facility is parent organization of: University of Coimbra Department of Chemistry NMR Core facility |
Free | nlx_155543, ISNI:0000 0000 9511 4342, Wikidata:Q368643, Crossref funder ID:501100007474, grid.8051.c | https://ror.org/04z8k9a98 | SCR_002842 | University of Coimbra, Universidade de Coimbra | 2026-07-25 12:05:32 | 0 | ||||||
|
General Clinical Research Centers Program Resource Report Resource Website 10+ mentions |
General Clinical Research Centers Program (RRID:SCR_002847) | GCRC | funding resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities. | clinical research program, career development |
has parent organization: National Center for Research Resources has parent organization: National Institutes of Health |
NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25308 | SCR_002847 | General Clinical Research Centers, General Clinical Research Centers (GCRC) | 2026-07-25 12:05:32 | 35 | ||||||
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CVXOPT - Python Software for Convex Optimization Resource Report Resource Website 1+ mentions |
CVXOPT - Python Software for Convex Optimization (RRID:SCR_002918) | CVXOPT | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Pythons extensive standard library and on the strengths of Python as a high-level programming language. Current version includes the following features: * efficient Python classes for dense and sparse matrices (real and complex), with Python indexing and slicing and overloaded operations for matrix arithmetic * an interface to most of the double-precision real and complex BLAS * an interface to LAPACK routines for solving linear equations and least-squares problems, matrix factorizations (LU, Cholesky, LDLT and QR), symmetric eigenvalue and singular value decomposition, and Schur factorization * an interface to the fast Fourier transform routines from FFTW * interfaces to the sparse LU and Cholesky solvers from UMFPACK and CHOLMOD * routines for linear, second-order cone, and semidefinite programming problems * routines for nonlinear convex optimization * interfaces to the linear programming solver in GLPK, the semidefinite programming solver in DSDP5, and the linear, quadratic and second-order cone programming solvers in MOSEK * a modeling tool for specifying convex piecewise-linear optimization problems. A platform-independent source package and a binary Windows installer are available from the Download section. CVXOPT is also available precompiled for the major platforms: * Debian Linux * Ubuntu Linux * Fedora Linux * Python(x,y) for Microsoft Windows CVXOPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. | convex optimization, python | has parent organization: University of California at Los Angeles; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30018 | SCR_002918 | CVXOPT - Python Software for Convex Optimization | 2026-07-25 12:05:34 | 2 | |||||||
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Brazilian Ministry of Science Technology and Innovation Resource Report Resource Website 1+ mentions |
Brazilian Ministry of Science Technology and Innovation (RRID:SCR_002876) | MCTI, MCT | government granting agency | is parent organization of: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil | SCR_002876 | Tecnologia e Inovação, Ministry of Science Technology and Innovation (Brazil), Ministério da Ciência, Ministério da Ciência e Tecnologia - Brazil, Ministry of Science and Technology (Brazil) | 2026-07-25 12:05:33 | 7 | |||||||||||
|
British Heart Foundation Resource Report Resource Website 100+ mentions |
British Heart Foundation (RRID:SCR_002905) | BHF | institution | British charity and fundraiser for cardiovascular research. | cardiovascular research, coronary heart disease, fundraising | Crossref funder ID: 501100000274, ISNI: 0000 0001 0540 7035, nlx_82345, grid.452924.c, Wikidata: Q4970039 | https://ror.org/02wdwnk04 | SCR_002905 | 2026-07-25 12:05:34 | 130 | |||||||||
|
University of Cologne; Cologne; Germany Resource Report Resource Website 1+ mentions |
University of Cologne; Cologne; Germany (RRID:SCR_002903) | UoC | university | Public university in Germany that offers degrees in law, management and business, the arts and humanities, and human sciences. | public university, germany, degree program |
is parent organization of: TargetCaller is parent organization of: CGARS is parent organization of: ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins is parent organization of: Dictyostelium discoideum genome database is parent organization of: Gentle is parent organization of: Dictyostelium discoideum genome database is parent organization of: University of Cologne Center for Genomics (CCG) Core Facility |
grid.6190.e, ISNI:0000 0000 8580 3777, Wikidata:Q54096, nlx_14953 | https://ror.org/00rcxh774 | http://www.portal.uni-koeln.de/uoc_home.html?&L=1 | SCR_002903 | University of Cologne, Universitat zu Koln | 2026-07-25 12:05:33 | 2 | ||||||
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CNVassoc Resource Report Resource Website 1+ mentions |
CNVassoc (RRID:SCR_002901) | software resource | Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21609482 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02609 | SCR_002901 | CNVassoc: Association analysis of CNV data | 2026-07-25 12:05:34 | 1 | |||||||
|
University of Colorado Boulder; Colorado; USA Resource Report Resource Website 1+ mentions |
University of Colorado Boulder; Colorado; USA (RRID:SCR_003114) | university | Public university that offers degrees in the sciences, humanities, and social sciences. | university, research university, public university, colorado, degree |
is related to: Beta Cell Biology Consortium is related to: ELOKA has parent organization: University of Colorado; Colorado; USA is parent organization of: University of Colorado at Boulder Labs and Facilities is parent organization of: Community Surface Dynamics Modeling System is parent organization of: National Snow and Ice Data Center is parent organization of: IMOD is parent organization of: University of Colorado at Boulder, Department of Neuroscience is parent organization of: NeuraLinksPlus is parent organization of: Emergent is parent organization of: Standalone hamming is parent organization of: CU Boulder Electron Microprobe Laboratory is parent organization of: CU Boulder Institute for Behavioral Genetics is parent organization of: SeqTrace is parent organization of: QIIME is parent organization of: Colorado University at Boulder Shared Instrumentation in Nanofabrication and Characterization Core Facility is parent organization of: Colorado University at Boulder JILA Keck Lab and Fabrication Core Facility is parent organization of: Colorado University at Boulder Biochemistry Shared Instruments Pool Core Facility is parent organization of: Colorado University at Boulder Center for Infrastructure, Energy, and Space Testing Core Facility is parent organization of: Colorado University at Boulder Light Microscopy Core Facility is parent organization of: Colorado University at Boulder EM Services Core Facility is parent organization of: Colorado University at Boulder Green Labs Core Facility is parent organization of: Colorado University at Boulder Central Analytical Mass Spectrometry Core Facility is parent organization of: Colorado University at Boulder Intermountain Neuroimaging Consortium Core Facility is parent organization of: Colorado University at Boulder Green Labs Core Facility is parent organization of: Colorado University at Boulder BioChemistry Krios Electron Microscopy Core Facility is parent organization of: University of Colorado Boulder Chemical and Bio. Engineering instrument and electronics Core Facility is parent organization of: University of Colorado Boulder High Performance Computing PetaLibrary Core Facility is parent organization of: University of Colorado Boulder Earth Systems Stable Isotope Lab Core Facility is parent organization of: University of Colorado Boulder Organic Geochemistry Laboratory Core Facility is parent organization of: University of Colorado Boulder BioCore Core Facility is parent organization of: University of Colorado Boulder CU Thermochronology Research and Instrumentation Lab Core Facility is parent organization of: Colorado University at Boulder Soft Materials Research Center X-Ray Diffraction Facility Core Facility is parent organization of: University of Colorado Boulder Raman Microspectroscopy Lab Core Facility is parent organization of: Colorado University at Boulder Facility for Electron Microscopy of Materials Core Facility is parent organization of: Colorado University at Boulder Materials Instrumentation and Multimodal Imaging Core Facility is parent organization of: Colorado University at Boulder BioFrontiers Next-Gen Sequencing Facility Core Facility is parent organization of: Colorado University at Boulder Flow Cytometry Shared Core Facility is parent organization of: Colorado University at Boulder Macromolecular X-ray Crystallography Core Facility is parent organization of: University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Core Facility is parent organization of: Colorado University at Boulder High Throughput Screening Core Facility is parent organization of: University of Colorado Boulder Polymeric and Optical Materials Characterization Shared Core Facility is parent organization of: SHARCQ is parent organization of: University of Colorado Boulder Geomicrobiology Lab Core Facility is parent organization of: University of Colorado Boulder Intermountain Neuroimaging Consortium Core Facility is parent organization of: University of Colorado Boulder Biochemistry Nuclear Magnetic Resonance Core Facility |
Free, Freely available | nlx_10266 | https://ror.org/02ttsq026 | SCR_003114 | CU Boulder, UC Boulder, University of Colorado Boulder, CU-Boulder | 2026-07-25 12:05:37 | 3 | |||||||
|
SURPI Resource Report Resource Website 10+ mentions |
SURPI (RRID:SCR_003071) | SURPI | software resource | Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples. | pipeline, cloud based pipeline, pathogen identification |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
PMID:24899342 | OMICS_04623 | https://github.com/chiulab/surpi | SCR_003071 | Sequence-based Ultra-Rapid Pathogen Identification | 2026-07-25 12:05:37 | 13 | ||||||
|
FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-07-25 12:05:36 | 0 | ||||||
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pFind Resource Report Resource Website 100+ mentions |
pFind (RRID:SCR_003011) | software resource | A search engine system for automated peptide and protein identification from tandem mass spectra. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:17702057 | OMICS_02467 | SCR_003011 | 2026-07-25 12:05:36 | 118 | |||||||||
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Genetic Analysis Package Resource Report Resource Website 1+ mentions |
Genetic Analysis Package (RRID:SCR_003006) | software resource | GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates. | genetic, analysis, package, data, population, family, calculation, family, disease, aggregation, kinship, environmental, covariate, haplotype, marker | nif-0000-30271 | SCR_003006 | GAP | 2026-07-25 12:05:36 | 1 | ||||||||||
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tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-07-25 12:05:36 | 4 | ||||||
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Isopat Resource Report Resource Website |
Isopat (RRID:SCR_003025) | software resource | Software function that calculates the isotopic pattern (fine structures) for a given chemical formula. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_02409 | https://isopat.sourceforge.net/ | SCR_003025 | isopat: Calculation of isotopic pattern for a given molecular formula | 2026-07-25 12:05:35 | 0 | |||||||
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BRAIN Resource Report Resource Website 10+ mentions |
BRAIN (RRID:SCR_003018) | software resource | Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23350948 | GNU General Public License, v2 | biotools:brain, OMICS_02410 | https://bio.tools/brain | SCR_003018 | Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN | 2026-07-25 12:05:37 | 44 | ||||||
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SASqPCR Resource Report Resource Website 1+ mentions |
SASqPCR (RRID:SCR_003056) | software resource | All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required. | standalone software, computation, analysis, statistics, rt-qpcr, cdna, mrna, gene expression, quantification, reference gene, normalization, sas |
is listed by: OMICtools has parent organization: Google Code |
PMID:22238653 | Free, Available for download, Freely available | OMICS_02375 | SCR_003056 | SASqPCR: robust and rapid analysis of RT-qPCR data in SAS | 2026-07-25 12:05:36 | 6 | |||||||
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SurvComp Resource Report Resource Website 50+ mentions |
SurvComp (RRID:SCR_003054) | survcomp | software resource | R package providing functions to assess and to compare the performance of risk prediction (survival) models. | differential expression, gene expression, visualization, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21903630 | Free, Available for download, Freely available | OMICS_02373 | SCR_003054 | survcomp - Performance Assessment and Comparison for Survival Analysis | 2026-07-25 12:05:37 | 58 |
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