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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software toolkit, software resource | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer, https://bio.tools/khmer, https://sources.debian.org/src/khmer/ | https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-08-15 11:29:36 | 25 | ||||
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Speed BioSystems Resource Report Resource Website |
Speed BioSystems (RRID:SCR_001673) | biomaterial supply resource, material resource | Commercial antibody supplier based in Maryland. | antibody supplier, maryland, commercial | Free, Freely Available | nlx_152465 | SCR_001673 | 2026-08-15 11:29:27 | 0 | ||||||||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software application, software resource | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-08-15 11:29:37 | 8 | ||||
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Jozef Stefan Institute; Ljubljana; Slovenia Resource Report Resource Website |
Jozef Stefan Institute; Ljubljana; Slovenia (RRID:SCR_000974) | JSI, IJS | training service resource, service resource | A scientific research institute that is involved with a broad spectrum of basic and applied research. Some of the areas they focus on include production and control technologies, communication and computer technology, and energy utilization and environmental science. They also engage in collaborations to develop medical equipment and new diagnostic methods into clinical medicine. | institute, scientific research, production technology, control technology, biotechnology, environmental technology, nanotechnology, nuclear engineering, collaboration, medical equipment, isotopes, clinical research, diagnostic, clinical medicine |
is parent organization of: VideoLectures.NET is parent organization of: SEGS is parent organization of: GoMapMan |
nlx_153883 | SCR_000974 | Institut Joef Stefan, Jozef Stefan Institute | 2026-08-15 11:29:36 | 0 | ||||||||
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BEAGLE Resource Report Resource Website 1000+ mentions |
BEAGLE (RRID:SCR_001789) | BEAGLE | software application, software resource | Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac). | gene, genetic, genomic, java, ms-windows, linux, unix, solaris, macos, identity by descent, genotype, haplotype |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:17924348 PMID:17326099 PMID:21310274 DOI:10.1086/521987 |
Free, Available for download, Freely available | nlx_154238, OMICS_00052, OMICS_00201 | https://sources.debian.org/src/beagle/ | https://www.stat.auckland.ac.nz/%7Ebrowning/beagle/beagle.html | SCR_001789 | BEAGLE Genetic Analysis Software Package | 2026-08-15 11:29:39 | 2377 | ||||
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nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software application, standalone software, software resource | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
NCI CA009363; NCI CA138249; NHGRI HG006853; Edelman-Gardner Foundation |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-08-15 11:29:27 | 1 | |||||
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CYRILLIC Resource Report Resource Website 50+ mentions |
CYRILLIC (RRID:SCR_001823) | Cyrillic | software application, commercial organization, software resource | Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages. | gene, genetic, genomic, visual c++, ms-windows, pedigree, linkage analysis, risk analysis, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software |
PMID:1973333 | Free, Available for download, Freely available | nlx_154279, OMICS_00208 | http://www.cyrillicsoftware.com | SCR_001823 | CyrillicSoftware | 2026-08-15 11:29:27 | 52 | |||||
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Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure Resource Report Resource Website 10+ mentions |
Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) | SCORE imaging | data or information resource, narrative resource | Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields. | format, authoring tool, embryo, microscopy, publishing format, image |
is listed by: FORCE11 has parent organization: Mayo Clinic Minnesota; Minnesota; USA has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NIGMS GM63904; NIDA DA14546 |
PMID:20528262 | nif-0000-07749 | SCR_001300 | Specimen in a Corrected Optical Rotational Enclosure imaging | 2026-08-15 11:29:26 | 11 | ||||||
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AnaSpec Resource Report Resource Website 1000+ mentions |
AnaSpec (RRID:SCR_002114) | biomaterial supply resource, material resource | Commercial supplier of antibodies, reagents, and dyes for research. | antibody supply company, reagent producer | Restricted | nlx_152270 | SCR_002114 | AnaSpec Inc, EGT Group | 2026-08-15 11:29:40 | 2089 | |||||||||
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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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