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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software toolkit, software resource | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-08-15 11:29:27 | 72 | ||||||
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Computational Morphometry Toolkit Resource Report Resource Website 10+ mentions |
Computational Morphometry Toolkit (RRID:SCR_002234) | CMTK | software toolkit, software application, software resource | A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished. | reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: neurodebian |
Free, Available for download, Freely available | nlx_155536 | http://www.nitrc.org/projects/cmtk, https://sources.debian.org/src/cmtk/ | SCR_002234 | Computational Morphometry Toolkit (CMTK) | 2026-08-15 11:29:27 | 38 | ||||||
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CLUSTAG Resource Report Resource Website 1+ mentions |
CLUSTAG (RRID:SCR_001816) | CLUSTAG | software application, software resource | Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment. | gene, genetic, genomic, java, hierarchical clustering, single nucleotide polymorphism, windows, unix |
is listed by: Genetic Analysis Software has parent organization: Hong Kong Baptist University; Hong Kong; China |
PMID:15585525 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154273 | http://hkumath.hku.hk/web/link/CLUSTAG/CLUSTAG.html | SCR_001816 | CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs | 2026-08-15 11:29:39 | 1 | |||||
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OpenBioinformatics.org Resource Report Resource Website 10+ mentions |
OpenBioinformatics.org (RRID:SCR_002229) | OpenBioinformatics.org | software repository, software resource | An open bioinformatis software repository with no tie to any organization or institution. Contact them to host your software. | bioinformatics, software |
is related to: PennCNV is parent organization of: ANNOVAR is parent organization of: GenGen |
Free, Available for download, Freely available | nlx_155524 | SCR_002229 | OpenBioinformatics.org: An open bioinformatis software repository | 2026-08-15 11:29:40 | 11 | |||||||
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TheDataWeb and DataFerrett Resource Report Resource Website 1+ mentions |
TheDataWeb and DataFerrett (RRID:SCR_003197) | DataFerrett | software application, text-mining software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2025. A data analysis and extraction tool from the US Census Bureaus with recoding capabilities to customize federal, state, and local data to suit your requirements. DataFerret works with the DataWeb, a network of online data libraries and an infrastructure for intelligent browsing. TheDataweb provides easy access to data from disparate locations across the internet using DataFerrett as its interface. It brings together demographic, economic, environmental, health, and other datasets that are usually separated by geography and/or organization.Using DataFerrett, you can develop an unlimited array of customized spreadsheets that are as versatile and complex as your usage demands. For a listing/description of datasets available using the DataFerrett refer to the Datasets Available tab. DataFerrett helps you locate and retrieve the data you need across the Internet to your desktop or system, regardless of where the data resides. You can develop and customize tables and select the results to create a graph or map for a visual depiction of your data. You can also save your data in the databasket and save the table you have created for reuse. The DataFerrett tool can use a java applet through an internet browser or be installed as an application on your desktop. The DataFerrett Applet requires you to have popup windows enabled in your browser for this website to function properly. | data mining, data extraction, data analysis, economics, health, demographics, education, census, statistics, employment, unemployment, federal, state, local, transportation, housing, economic, environment, demography | has parent organization: U.S. Census Bureau | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00616 | SCR_003197 | Data Federated Electronic Research Review Extraction and Tabulation Tool, TheDataWeb/DataFerrett, TheDataWeb for the DataFerrett, DataFerrett for TheDataWeb | 2026-08-15 11:29:41 | 3 | |||||||
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NIH Toolbox - Assessment of Neurological and Behavioral Function Resource Report Resource Website 100+ mentions |
NIH Toolbox - Assessment of Neurological and Behavioral Function (RRID:SCR_002423) | NIH Toolbox | assessment test provider, material resource | An integrated set of tools for measuring cognitive, emotional, motor and sensory function. These tools are being validated for use in diverse cultures, ethnic and geographic groups, ages (3-85 years) and study types. The toolbox is expected to provide a more complete picture of neurological and behavioral health in large-scale longitudinal studies, epidemiological studies, and clinical trials; and to facilitate cross-study comparisons. Moreover, the toolbox will: * be minimally burdensome to subjects and investigators, * utilize state-of-the art psychometric approaches and technology, including computer-assisted evaluation, and * be dynamic and adaptable to changes in measurement and technology. * be available in English and Spanish Many clinical studies collect data on aspects of neurological and behavioral function. However, the neurological and behavioral tests currently available to researchers lack uniformity and often require specialized training to administer. These limitations make it difficult to compile data across the full range of normal neurological function, and to compare data across studies. The toolbox is royalty-free and is expected to be available online by summer 2012. | cognitive, motor, emotional, sensory, epidemiology, prevention, computerized adaptive testing, disease, cognition, executive function, episodic memory, working memory, speed, language, attention, emotion, negative affect, positive affect, stress, coping, social, relationship, motor, locomotion, strength, non-vestibular, dexterity, endurance, sensation, vision, audition, vestibular, somatosensation, nneurological assessment, behavioral assessment, taste, olfaction, learning, memory, lexical retrieval, visuospatial ability, speed of processing, mood, adaptability, interpersonal relations, self-regulation, motor function, non-vestibular balance, hearing, vestibular balance, smell, touch, adult human, late adult human, child, psychometric test, measurement tool |
is related to: Pediatric Imaging Neurocognition and Genetics has parent organization: Northwestern University; Illinois; USA is parent organization of: NIH Toolbox Picture Vocabulary Test is parent organization of: NIH Toolbox Words-in Noise Test is parent organization of: NIH Toolbox Dimensional Change Card Sort Test is parent organization of: NIH Toolbox Flanker Inhibitory Control and Attention Test is parent organization of: NIH Toolbox Picture Sequence Memory Test is parent organization of: NIH Toolbox Auditory Verbal Learning Test (Rey) is parent organization of: NIH Toolbox 9-Hole Pegboard Dexterity Test is parent organization of: NIH Toolbox Oral Reading Recognition Test is parent organization of: NIH Toolbox Pattern Comparison Processing Speed Test is parent organization of: NIH Toolbox Oral Symbol Digit Test is parent organization of: NIH Toolbox List Sorting Working Memory Test is parent organization of: NIH Toolbox Standing Balance Test is parent organization of: NIH Toolbox 2-Minute Walk Endurance Test is parent organization of: NIH Toolbox 4-Meter Walk Gait Speed Test is parent organization of: NIH Toolbox Grip Strength Test is parent organization of: NIH Toolbox Odor Identification Test is parent organization of: NIH Toolbox Pain Interference Survey is parent organization of: NIH Toolbox Pain Intensity Survey is parent organization of: NIH Toolbox Regional Taste Intensity Test is parent organization of: NIH Toolbox Dynamic Visual Acuity Test is parent organization of: NIH Toolbox Visual Acuity Test |
WO HHS-N-260-2006-00007-C | Free, Available for download, Freely available | nif-0000-00393 | SCR_002423 | NIH Toolbox - Assessment of Neurological Behavioral Function, NIH Toolbox for Assessment of Neurological and Behavioral Function, NIH Toolbox for the Assessment of Neurological and Behavioral Function | 2026-08-15 11:29:38 | 105 | ||||||
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NIH Toolbox 4-Meter Walk Gait Speed Test Resource Report Resource Website |
NIH Toolbox 4-Meter Walk Gait Speed Test (RRID:SCR_003632) | assessment test provider, material resource | Assessment test to measure gait speed where participants are asked to walk a short distance (4 meters) at their usual pace. Participants complete one practice and then two timed trials. Raw scores are recorded as the time in seconds required to walk 4 meters on each of the two trials, with the better trial used for scoring. The 4-Meter Walk Gait Speed Test is adapted from the 4-meter walk test in the Short Physical Performance Battery. The test takes approximately 3 minutes to administer (including instructions and practice). This test is recommended for ages 7-85. | motor, locomotion, gait, speed | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157782 | SCR_003632 | 4-Meter Walk Gait Speed Test | 2026-08-15 11:29:42 | 0 | |||||||||
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NIH Toolbox 2-Minute Walk Endurance Test Resource Report Resource Website |
NIH Toolbox 2-Minute Walk Endurance Test (RRID:SCR_003631) | assessment test provider, material resource | Assessment test that measures sub-maximal cardiovascular endurance by recording the distance that the participant is able to walk on a 50-foot (out and back) course in 2 minutes. The participant's raw score is the distance in feet and inches walked in 2 minutes. The test is adapted from the American Thoracic Society's 6-Minute Walk Test Protocol. The test overall takes approximately 4 minutes to administer (with instructions and practice). This test is recommended for ages 3-85. | motor, endurance, cardiovascular | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157781 | SCR_003631 | 2-Minute Walk Endurance Test | 2026-08-15 11:29:29 | 0 | |||||||||
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VennDiagram Resource Report Resource Website 1000+ mentions |
VennDiagram (RRID:SCR_002414) | software toolkit, software resource | Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure. | Venn and Euler plots, mac os x, unix/linux, windows, r |
is listed by: OMICtools is listed by: Debian is related to: jVenn has parent organization: CRAN |
PMID:21269502 | Free, Available for download, Freely available | OMICS_05570 | https://sources.debian.org/src/r-cran-venndiagram/ | SCR_002414 | VennDiagram: Generate high-resolution Venn and Euler plots | 2026-08-15 11:29:40 | 2138 | ||||||
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NIH Toolbox Standing Balance Test Resource Report Resource Website |
NIH Toolbox Standing Balance Test (RRID:SCR_003628) | assessment test provider, material resource | A measure to assess static standing balance that involves the participant assuming and maintaining up to 5 poses for 50 seconds each. The sequence of poses is: eyes open on a solid surface, eyes closed on solid surface, eyes open on foam surface, eyes closed on foam surface, eyes open in tandem stance. Detailed stopping rules are in place to ensure participant safety with these progressively demanding poses. Postural sway is recorded for each pose using an accelerometer that the participant wears at waist level. This test takes approximately 7 minutes to administer and is recommended for ages 3-85. | motor, balance | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157779 | SCR_003628 | Standing Balance Test | 2026-08-15 11:29:39 | 0 | |||||||||
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Template-O-Matic Toolbox Resource Report Resource Website 10+ mentions |
Template-O-Matic Toolbox (RRID:SCR_003220) | TOM Toolbox, TOM | software toolkit, software resource | Software toolbox for creating customized pediatric templates. It provides reference data based on imaging data from the NIH study of normal brain development. Using the general linear model, they statistically isolate the influence of external variables of interest on brain structure, allowing us to generate high-quality matched templates for any given group of subjects. The toolbox offers two options: # to create pediatric templates (T1) and tissue maps (GM, WM, and CSF) based on the objective 1 NIH data (n = 404), in the age range of 5-18 years, or # to assess a new reference population with regard to your variables of interest. Of note, this approach is generally applicable and in no way restricted to analyzing pediatric imaging data: for example, if you aim at investigating the effects of aging in elderly subjects, the toolbox will also allow you to create more appropriate reference (if your group is large enough to isolate such effects). | reference, pediatric, neuroimaging, template | PMID:18424084 | Free, Available for download, Freely available | nlx_157256 | http://dbm.neuro.uni-jena.de/software/tom/ | SCR_003220 | Template-O-Matic | 2026-08-15 11:29:39 | 12 | ||||||
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MUMA Resource Report Resource Website 10+ mentions |
MUMA (RRID:SCR_002412) | MUMA | software application, standalone software, software resource | Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY). | standalone software, mac os x, unix/linux, windows, r, metabolomics, univariate, multivariate, data analysis |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_03370 | SCR_002412 | Metabolomics Univariate and Multivariate Analysis (MUMA), Metabolomic Univariate and Multivariate Analysis | 2026-08-15 11:29:38 | 28 | |||||||
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RFT FDR Resource Report Resource Website |
RFT FDR (RRID:SCR_002533) | RFT_FDR | software application, software resource | So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171). | console (text based), gnome, kde, matlab, mgh/mgz, modeling, magnetic resonance, os independent, rendering, statistical operation, surface analysis, surface rendering, thickness, visualization, random field theory |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FreeSurfer |
Free, Available for download, Freely available | nlx_155938 | SCR_002533 | RFT-FDR, RFT FDR | 2026-08-15 11:29:40 | 0 | |||||||
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NIH Toolbox Oral Reading Recognition Test Resource Report Resource Website |
NIH Toolbox Oral Reading Recognition Test (RRID:SCR_003622) | assessment test provider, material resource | Assessment test that measures the ability of patients to identify words and letters. The participant is asked to read and pronounce letters and words as accurately as possible. The test administrator scores them as right or wrong. For the youngest children, the initial items require them to identify letters (as opposed to symbols) and to identify a specific letter in an array of 4 symbols. The test is given in a computerized adaptive format and requires approximately 3 minutes. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested. Separate but parallel reading tests have been developed in English and in Spanish. | cognition, language | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | nlx_157774 | SCR_003622 | Oral Reading Recognition Test | 2026-08-15 11:29:41 | 0 | |||||||||
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Source BioScience LifeSciences Resource Report Resource Website 50+ mentions |
Source BioScience LifeSciences (RRID:SCR_003344) | RZPD | biomaterial supply resource, material resource | Source BioScience LifeSciences are European leaders in DNA sequencing, genomic services, bioinformatic analyses and offers a comprehensive portfolio of genomic reagents and antibodies. Source BioScience LifeScience is a CPA, GLP/GCP accredited and Illumina NGS CSPro certified genomic service provider and distributes a comprehensive range of biological products to companies and institutions worldwide. Source BioScience is proud to announce that Source BioScience imaGenes has joined it's LifeSciences group. This will enable us to bring our customers one unified website with our complete range of Products, Clones and Services. We have merged our clone libraries together so that can now offer you over 20 million clones! Add to this our excellent sequencing service and our range of over 100,000 antibodies and Source BioScience LifeSciences is your ideal outsourcing partner. | clones, libraries, microarray, dna sequencing, rna interference, next generation sequencing, proteomics | is listed by: One Mind Biospecimen Bank Listing | Free, Freely available | nif-0000-31984 | https://sourcebioscience.com/ | SCR_003344 | imaGenes, Source BioScience imaGenes | 2026-08-15 11:29:39 | 72 | ||||||
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Mount Sinai Allograft Technologies Resource Report Resource Website |
Mount Sinai Allograft Technologies (RRID:SCR_003586) | biomaterial supply resource, material resource | Mount Sinai Allograft Technologies, a department of Mount Sinai Hospital formerly known as the The Rubinoff Bone Bank, has been a leader in advanced tissue innovations since 1972. We are committed to providing the highest quality bone and tissue allograft products as well as continued innovation in the development of allograft implants for transplantation. We are dedicated to meeting all surgical needs and to exceed all client expectations. We work closely with the Trillium Gift of Life Network to promote their mission of increasing donor awareness and to ensure that the wishes of Ontario donor families' are carried out with the utmost care and respect. Our allograft implants are 100% Ontario produced, human allograft tissues. To produce the safest and highest quality Canadian produced allograft implants, Mount Sinai Allograft Technologies leverages the expertise of a variety of medical experts, state-of-the art laboratory testing, proven bio-processing techniques, validated irradiation methods and preferred packaging systems. | is listed by: One Mind Biospecimen Bank Listing | nlx_12054 | SCR_003586 | The Rubinoff Bone Bank, Rubinoff Bone Bank | 2026-08-15 11:29:39 | 0 | ||||||||||
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NIRx2nirs: A NIRx to .nirs data converter Resource Report Resource Website 1+ mentions |
NIRx2nirs: A NIRx to .nirs data converter (RRID:SCR_002492) | NIRx2nirs | software application, software resource | A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge. | hardware, nirs, fnir, optical imaging, optical imaging, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Homer2 |
Free, Available for download, Freely available | nlx_155887 | SCR_002492 | 2026-08-15 11:29:28 | 1 | ||||||||
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ProLinks Database of Functional Linkages Resource Report Resource Website |
ProLinks Database of Functional Linkages (RRID:SCR_003185) | software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage. | functional linkage, protein linkage, inference method |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:15128449 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00580 | http://prl.mbi.ucla.edu/prlbeta/prolinks.jsp http://dip.mbi.ucla.edu/dipbeta/prolinks.jsp | SCR_003185 | Prolinks | 2026-08-15 11:29:39 | 0 | ||||||
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MBF BioScience: Stereo Investigator Resource Report Resource Website 100+ mentions |
MBF BioScience: Stereo Investigator (RRID:SCR_002526) | instrument resource, software resource | Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology. | stereology, MBF Bioscience, number, length, area, volume cells, biological structures, tissue specimen |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
Restricted | SciRes_000114, SCR_024705, SCR_018948 | http://www.nitrc.org/projects/si_stereology | SCR_002526 | Stereo Investigator system | 2026-08-15 11:29:38 | 162 | |||||||
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Primate Embryo Gene Expression Resource Resource Report Resource Website 1+ mentions |
Primate Embryo Gene Expression Resource (RRID:SCR_002765) | PREGER | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods. | primate, embryo, gene, expression, embryologist, microarray, rhesus, monkey, oocyte, embryo, cdna, library, molecular, analysis, stem cell, oocyte quality, preimplantation development, transcription |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Temple University School of Medicine; Pennsylvania; USA |
NIH Office of the Director R24 OD012221; NCRR RR15253 |
PMID:14724133 PMID:17147927 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24366 | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources | SCR_002765 | PREGER Online, Preger.org | 2026-08-15 11:29:28 | 6 |
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