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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SaskPrimerFS Resource Report Resource Website |
SaskPrimerFS (RRID:SCR_003159) | SaskPrimerFS | software resource | Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism. | gene family, pcr primer, pcr, primer, dna sequence, command-line, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02335 | SCR_003159 | 2026-02-14 02:00:41 | 0 | ||||||||
|
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 | 2026-02-14 02:00:40 | 6981 | |||||||||
|
Biological Collections Ontology Resource Report Resource Website |
Biological Collections Ontology (RRID:SCR_003262) | BCO | data or information resource, ontology, controlled vocabulary | Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. | owl, interoperability, biodiversity, museum collection, environmental sample, metagenomic sample, ecological survey |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
PMID:24595056 | Free, Available for download, Freely available | nlx_157333 | http://purl.obolibrary.org/obo/bco.owl http://purl.bioontology.org/ontology/BCO |
SCR_003262 | 2026-02-14 02:00:24 | 0 | ||||||
|
MorphoBank Resource Report Resource Website 100+ mentions |
MorphoBank (RRID:SCR_003213) | MorphoBank | data or information resource, database | Web application providing online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). It enables researchers to upload images and affiliate data with those images (labels, species names, etc.) and allows researchers to upload morphological data and affiliate it with phylogenetic matrices. MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived. | phenotype, web service, phylogenetics, cladistics, histology, neurology, taxonomy, image, phylogeny, cladistic analysis, morphology, anatomy, evolution, homology, systems biology, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: Stony Brook University; New York; USA |
NSF ; NOAA NA04OAR4700191 |
PMID:34875801 | Free, Freely available | DOI:10.25504/FAIRsharing.1y63n8, DOI:10.17616/R3PC7F, DOI:10.7934, nlx_156938, r3d100010786 | https://doi.org/10.17616/R3PC7F https://doi.org/10.17616/r3pc7f https://doi.org/10.7934/ https://dx.doi.org/10.7934/ https://fairsharing.org/10.25504/FAIRsharing.1y63n8 https://doi.org/10.17616/R3MK88 |
SCR_003213 | 2026-02-14 02:00:30 | 113 | |||||
|
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 | 2026-02-14 02:00:30 | 6 | |||||||
|
Allele Biotechnology Resource Report Resource Website 1+ mentions |
Allele Biotechnology (RRID:SCR_003164) | Allele Biotech | commercial organization | A private company offering a wide variety of Molecular Biology reagents, fluorescent proteins, luciferase assay substrates, genotyping kits, and various custom services. The company isalso in the RNAi field with its recent patents in Pol III promoter-driven siRNA, shRNA, and miRNA. They introduced high titer lentivirus, camelid antibodies, and cell based assays and also offer Baculovirus protein expression and Gryphon retrovirus systems. | molecular biology, reagent, fluorescent protein, luciferase assay substrate, genotyping kit, custom service | is related to: Phoenix | Free, Available for download, Freely available | nlx_156865 | SCR_003164 | Allele Biotechnology and Pharmaceuticals Inc | 2026-02-14 02:00:30 | 1 | |||||||
|
American Association for the History of Medicine Resource Report Resource Website |
American Association for the History of Medicine (RRID:SCR_003161) | AAHM | nonprofit organization | A professional association of historians, physicians, nurses, archivists, curators, librarians, and others that promotes and encourages research, study, writing, and interest in the history of medicine and allied fields. | history, medicine | Free, Freely available | nlx_156861, grid.486311.9 | https://ror.org/04w1hax42 | SCR_003161 | 2026-02-14 02:00:23 | 0 | ||||||||
|
Lipid Ontology Resource Report Resource Website |
Lipid Ontology (RRID:SCR_003349) | LiPrO | data or information resource, ontology, controlled vocabulary | An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied. | owl, lipid, ontology |
is listed by: BioPortal is listed by: OBO |
Free, Available for download, Freely available | nlx_157458 | http://www.lipidprofiles.com/LipidOntology | SCR_003349 | 2026-02-14 02:00:32 | 0 | |||||||
|
Fisher BioReagents Resource Report Resource Website 1000+ mentions |
Fisher BioReagents (RRID:SCR_003374) | commercial organization | An Antibody supplier | Free, Freely available | nlx_152364 | SCR_003374 | 2026-02-14 02:00:26 | 1474 | |||||||||||
|
Measurement Method Ontology Resource Report Resource Website |
Measurement Method Ontology (RRID:SCR_003373) | MMO | data or information resource, ontology, controlled vocabulary | An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms. | obo, phenotype, clinical |
is listed by: SourceForge is listed by: BioPortal is listed by: OBO |
PMID:22654893 | Free, Available for download, Freely available | nlx_157468 | http://sourceforge.net/projects/phenoonto/ ftp://rgd.mcw.edu/pub/ontology/measurement_method/measurement_method.obo |
SCR_003373 | 2026-02-14 02:00:47 | 0 | ||||||
|
JobTarget Resource Report Resource Website |
JobTarget (RRID:SCR_003365) | JobTarget | job resource | JobTarget is the foundation upon which careers and companies are built. Our technology and services connect millions of job seekers to hundreds of thousands of companies through thousands of job boards. We facilitate faster, more meaningful connections by powering niche job sites that target specific audiences of talent, and providing technology and advertising solutions for employers to more quickly and cost-effectively locate the most qualified candidates for their openings. Explore our Products & Services to experience the JobTarget difference or check out Who We Serve to narrow in on the best solutions to serve you. | Free, Freely available | nlx_11196 | https://www.jobtarget.com/ | SCR_003365 | 2026-02-14 02:00:46 | 0 | |||||||||
|
ALDEx2 Resource Report Resource Website 500+ mentions |
ALDEx2 (RRID:SCR_003364) | software resource | Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: aldex has parent organization: Western University; Ontario; Canada |
PMID:24910773 | Free, Available for download, Freely available | biotools:aldex2, OMICS_04634 | https://bio.tools/aldex2 | SCR_003364 | 2026-02-14 02:00:32 | 529 | |||||||
|
Malaria Ontology Resource Report Resource Website |
Malaria Ontology (RRID:SCR_003369) | IDOMAL | data or information resource, ontology, controlled vocabulary | An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO). | obo, health, pathological, clinical, epidemiological, biological, intervention |
is listed by: BioPortal is listed by: OBO has parent organization: AnoBase: An Anopheles database |
Malaria | Free, Available for download, Freely available | nlx_157464 | http://purl.obolibrary.org/obo/idomal.obo http://anobase.vectorbase.org/idomal/IDOMAL.obo |
SCR_003369 | 2026-02-14 02:00:32 | 0 | ||||||
|
RCircos Resource Report Resource Website 100+ mentions |
RCircos (RRID:SCR_003310) | software resource | Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: shinyCircoss has parent organization: CRAN has parent organization: Bitbucket |
PMID:23937229 | Free, Available for download, Freely available | OMICS_04661 | https://bitbucket.org/henryhzhang/rcircos/ | SCR_003310 | RCircos: Circos 2D Track Plot | 2026-02-14 02:00:25 | 245 | ||||||
|
JCVI Primer Designer Resource Report Resource Website 1+ mentions |
JCVI Primer Designer (RRID:SCR_003275) | JCVI Primer Designer | software resource | High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. | perl, command-line, pcr primer design, pcr, primer, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18405373 | Free, Available for download, Freely available | OMICS_02330 | SCR_003275 | 2026-02-14 02:00:44 | 1 | |||||||
|
ddCt Resource Report Resource Website 100+ mentions |
ddCt (RRID:SCR_003396) | ddCt | software resource | Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions. | differential expression, gene expression, microtitre plate assay, q-pcr |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02312 | SCR_003396 | Delta-Delta-Ct | 2026-02-14 02:00:48 | 321 | |||||||
|
ggbio Resource Report Resource Website 10+ mentions |
ggbio (RRID:SCR_003313) | software resource | An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | standalone software, unix/linux, mac os x, windows, r, infrastructure, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22937822 | Free, Available for download, Freely available | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/ https://bio.tools/ggbio |
SCR_003313 | ggbio - Visualization tools for genomic data | 2026-02-14 02:00:45 | 14 | ||||||
|
Dictyostelium Discoideum Anatomy Ontology Resource Report Resource Website |
Dictyostelium Discoideum Anatomy Ontology (RRID:SCR_003309) | DDANAT | data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum. | obo, anatomy, organismal, cellular |
is listed by: BioPortal is listed by: OBO has parent organization: Dictyostelium discoideum genome database |
Free, Available for download, Freely available | nlx_157387 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/microbial_gross_anatomy/dictyostelium/dictyostelium_anatomy.obo | SCR_003309 | Dictyostelium discoideum anatomy | 2026-02-14 02:00:45 | 0 | ||||||
|
NormFinder Resource Report Resource Website 1000+ mentions |
NormFinder (RRID:SCR_003387) | NormFinder | software resource | Software for identifying the optimal normalization gene among a set of candidates. It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design. It can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis. NormFinder.xla adds the NormFinder functionality directly to Excel. A version for R is also available. | normalization, gene |
is used by: RefFinder is listed by: OMICtools |
PMID:15289330 | Free, Available for download, Freely available | OMICS_02317 | https://www.moma.dk/software/normfinder | SCR_003387 | NormFinder software - Determine the optimal normalization gene | 2026-02-14 02:00:47 | 2419 | |||||
|
Minimal Anatomical Terminology Resource Report Resource Website |
Minimal Anatomical Terminology (RRID:SCR_003385) | MAT | data or information resource, ontology, controlled vocabulary | An ontology of minimal set of terms for anatomy. | obo, anatomy, organismal, ontology |
is listed by: BioPortal is listed by: OBO has parent organization: eMouseAtlas |
Free, Available for download, Freely available | nlx_157480 | http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/multispecies/minimal_anatomical_terminology.obo | SCR_003385 | 2026-02-14 02:00:47 | 0 |
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