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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-01 12:01:57 | 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 | 2026-08-01 12:02:20 | 2 | ||||||
|
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 | 2026-08-01 12:01:57 | 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 | 2026-08-01 12:02:02 | 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 | 2026-08-01 12:02:16 | 13 | ||||||
|
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 | 2026-08-01 12:02:00 | 118 | |||||||||
|
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 | 2026-08-01 12:02:15 | 1 | ||||||||||
|
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 | 2026-08-01 12:02:00 | 4 | ||||||
|
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 | 2026-08-01 12:02:15 | 44 | ||||||
|
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 | 2026-08-01 12:02:01 | 6 | |||||||
|
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 | 2026-08-01 12:02:16 | 58 | ||||||
|
PacBioToCA Resource Report Resource Website 10+ mentions |
PacBioToCA (RRID:SCR_003044) | software resource | A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads. | standalone software | is listed by: OMICtools | PMID:22750884 | Free, Available for download, Freely available | OMICS_05093 | https://rhallpb.github.io/Applications/pacBioToCA.html | SCR_003044 | pacBioToCA (error correction via Celera Assembler) | 2026-08-01 12:02:16 | 13 | ||||||
|
Dana-Farber Cancer Institute Resource Report Resource Website 1+ mentions |
Dana-Farber Cancer Institute (RRID:SCR_003040) | DFCI | institution |
Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world. |
child, adult human, pediatric, young human |
has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: Spotfinder is parent organization of: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer is parent organization of: Gene Index Project is parent organization of: CistromeMap is parent organization of: BINOCh is parent organization of: Dana Farber Tissue Bank is parent organization of: CistromeFinder is parent organization of: TM4 is parent organization of: WorfDB is parent organization of: Predictive Networks is parent organization of: RamiGO is parent organization of: DFCI Animal Resources Facility is parent organization of: DFCI Biohazard Containment Core Facility is parent organization of: DFCI Biospecimen Repository Core Facility is parent organization of: DFCI Blais Proteomics Center is parent organization of: DFCI Clinical Research Laboratory is parent organization of: DFCI Survey and Data Management Core is parent organization of: DFCI Flow Cytometry Core Facility is parent organization of: DFCI Medical Arts Core Facility is parent organization of: DFCI Microarray Core Facility is parent organization of: Dana-Farber Cancer Institute Molecular Biology Core Facility is parent organization of: DFCI RNA Interference Screening Facility is parent organization of: DFCI Shannon McCormack Advanced Molecular Diagnostics Laboratory is parent organization of: MAnorm is parent organization of: NPS is parent organization of: DFCI Confocal and Light Microscopy Core Facility is parent organization of: DFCI Monoclonal Antibody Core Facility is parent organization of: Dana-Farber Cancer Institute Labs and Facilities is parent organization of: DFCI Center for Cancer Computational Biology is parent organization of: GeneSigDB is parent organization of: MACS is parent organization of: DGAP |
Cancer | NCI ; Jimmy Fund |
Free, Freely available | Crossref funder ID: 100007886, grid.65499.37, Wikidata: Q1159198, ISNI: 0000 0001 2106 9910, nif-0000-30432 | https://ror.org/02jzgtq86 | SCR_003040 | Dana Farber Cancer Institute, Dana-Farber | 2026-08-01 12:02:16 | 6 | ||||
|
Primer Designer Resource Report Resource Website 1+ mentions |
Primer Designer (RRID:SCR_003189) | Primer Designer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki. | primer, primer design |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02327 | https://www.thermofisher.com/us/en/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-design-tools.html?ef_id=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB:G:s&s_kwcid=AL!3652!3!683518170873!e!!g!!primer%20designer!20841448243!155985486683&cid=bid_mol_pch_r01_co_cp1358_pjt0000_bid00000_0se_gaw_nt_pur_con&gad_source=1&gad_campaignid=20841448243&gbraid=0AAAAADxi_GTCU-6xCgQrctnmtmtMSDEQj&gclid=Cj0KCQjw-NfDBhDyARIsAD-ILeBszOXU4wXumqZJ--N8Z5rguB5P2-7UmpEuidzHsK1sgSXJROQ3of8aAtkqEALw_wcB | SCR_003189 | 2026-08-01 12:02:28 | 2 | |||||||
|
SALT Resource Report Resource Website 1000+ mentions |
SALT (RRID:SCR_003187) | SALT | software resource | Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families. | next-generation sequencing, protein, protein domain, short read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23782615 | Free, Available for download, Freely available | OMICS_01565, biotools:salt | https://bio.tools/salt | SCR_003187 | SALT - Protein domain classifier | 2026-08-01 12:02:17 | 1294 | |||||
|
XORRO Resource Report Resource Website 1+ mentions |
XORRO (RRID:SCR_003181) | XORRO | software resource | Efficient paired-read overlap software program for use with Illumina sequencing. | illumina, next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01569 | SCR_003181 | XORRO: Rapid Paired-End Read Overlapper | 2026-08-01 12:02:17 | 1 | |||||||
|
mrCaNaVaR Resource Report Resource Website 10+ mentions |
mrCaNaVaR (RRID:SCR_003135) | mrCaNaVaR | software resource | Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals. | genome, next-generation sequence, duplication, deletion, copy number variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
Free, Freely available | OMICS_02138, nlx_156790, biotools:mrcanavar | https://bio.tools/mrcanavar | SCR_003135 | mrCaNaVaR - micro-read Copy Number Variant Regions, micro-read Copy Number Variant Regions | 2026-08-01 12:02:27 | 14 | ||||||
|
Laura and John Arnold Foundation Resource Report Resource Website 1+ mentions |
Laura and John Arnold Foundation (RRID:SCR_003240) | LJAF | institution | Private foundation whose funding activities are primarily centered around improving life in the United States. Its mission is to produce big and lasting changes in society over the long term. Their four areas of focus (2014) are: criminal justice, K-12 education, public accountability, and research integrity. | grant, criminal justice, k-12 education, public accountability, research integrity | Free, Freely available | Crossref funder ID: 100009827, ISNI: 0000 0004 0555 6315, nlx_157294, grid.480593.3, Wikidata: Q17088752 | https://www.arnoldventures.org/people/laura-arnold-john-arnold | SCR_003240 | Arnold Foundation | 2026-08-01 12:02:18 | 4 | |||||||
|
GeneCopoeia Resource Report Resource Website 5000+ mentions |
GeneCopoeia (RRID:SCR_003145) | commercial organization | Commercial organization which provides reagents and services for molecular biology research. Its services include clone collections, microRNA solutions, genome editing, qPCR products, and fluorescent labeling and detection. | reagent, pcr, clone, microrna, cell biology | Free, Freely available | nlx_152370 | SCR_003145 | GeneCopoeia Inc | 2026-08-01 12:02:27 | 6981 | |||||||||
|
Pipeliner Resource Report Resource Website 1+ mentions |
Pipeliner (RRID:SCR_003171) | software resource | Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24890372 | Free, Available for download, Freely available | OMICS_04844, biotools:pipeliner | https://bio.tools/pipeliner | SCR_003171 | 2026-08-01 12:02:28 | 6 |
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