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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PEPPER Resource Report Resource Website 1+ mentions |
PEPPER (RRID:SCR_000431) | PEPPER | software application, software resource | A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...). | plugin, protein-protein interaction, network, bio.tools |
is listed by: OMICtools is listed by: Cytoscape is listed by: bio.tools is listed by: Debian |
PMID:25138169 | Free, Available for download, Freely available | biotools:pepper, OMICS_05485 | https://bio.tools/pepper | SCR_000431 | Protein complex Expansion using Protein-Protein intERaction networks, Protein complex Expansion using Protein-Protein intERactions | 2026-08-09 09:02:58 | 1 | |||||
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EQTL EXPLORER Resource Report Resource Website 1+ mentions |
EQTL EXPLORER (RRID:SCR_001123) | EQTL EXPLORER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software) | gene, genetic, genomic, java | is listed by: Genetic Analysis Software | PMID:16357031 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154018 | SCR_001123 | 2026-08-09 09:03:09 | 2 | |||||||
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Corner Cube Environment Resource Report Resource Website |
Corner Cube Environment (RRID:SCR_001080) | software toolkit, image visualization software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. DOCUMENTED NOVEMBER 17, 2016: This program was removed on 03/18/15 and is not being monitored.A software visualization package for the symbolic display of functional neuroimaging datasets in an anatomical context. Written in IDL. | visualization, symbolic display, functional neuroimaging, dataset, anatomy, idl | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | PMID:9873900 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00282 | http://neurovia.umn.edu/distrib/cce.html | SCR_001080 | 2026-08-09 09:03:07 | 0 | |||||||
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dinifti Resource Report Resource Website 1+ mentions |
dinifti (RRID:SCR_000303) | dinifti | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format. | analyze, console (text based), dicom, format conversion, freebsd, linux, magnetic resonance, nifti, posix/unix-like |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: New York University; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155843 | http://www.nitrc.org/projects/dinifti, http://cbi.nyu.edu/software/dinifti.php, https://sources.debian.org/src/dicomnifti/ | SCR_000303 | NYU CBI DICOM to NIfTI Converter | 2026-08-09 09:02:56 | 2 | ||||||
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ShapeWorks Resource Report Resource Website 1+ mentions |
ShapeWorks (RRID:SCR_000424) | ShapeWorks | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results. | c++, console (text based), linux, macos, microsoft, magnetic resonance, posix/unix-like, rendering, shape analysis, surface rendering, visualization, win32 (ms windows), windows, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155961 | http://www.nitrc.org/projects/shapeworks | SCR_000424 | 2026-08-09 09:02:58 | 1 | ||||||
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NGSUtils Resource Report Resource Website 10+ mentions |
NGSUtils (RRID:SCR_001236) | NGSUtils | software toolkit, software resource | A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis. | mac os x, linux, next-generation sequencing, illumia, solid, 454, ion torrent, pac bio, sequencing, dna resequcing, rna resequcing, chip-seq, clip-seq, targeted resequencing, agilent exome capture, pcr targeting, dna, rna, mapping pipeline, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University School of Medicine; Indiana; USA |
PMID:23314324 | Free, Available for download, Freely available | biotools:ngsutils, OMICS_02104 | https://bio.tools/ngsutils | SCR_001236 | NGSUtils - Tools for next-generation sequencing analysis | 2026-08-09 09:03:08 | 40 | |||||
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TDT-PC Resource Report Resource Website |
TDT-PC (RRID:SCR_001116) | TDT-PC | software application, software resource | Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, ms-windows, ms-dos, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
PMID:11443734 | nlx_154677, biotools:tdt_power_calculator | https://bio.tools/tdt_power_calculator | SCR_001116 | Transmission Disequilibrium Test Power Calculator, TDT Power Calculator | 2026-08-09 09:03:09 | 0 | ||||||
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American Tissue Services Foundation - ATSF Resource Report Resource Website |
American Tissue Services Foundation - ATSF (RRID:SCR_000549) | ATSF | material resource, biomaterial supply resource | A non-profit organization that facilitates the donation of tissues. It supports healthcare agencies, coroners, medical examiners and funeral professionals through donations and training, as well as partnering with organizations that utilize tissue in medical care and research. | tissue, donation, healthcare, medicine, research | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_97074 | SCR_000549 | American Tissue Services Foundation | 2026-08-09 09:02:59 | 0 | ||||||||
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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 | 2026-08-09 09:03:10 | 25 | ||||
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PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden Resource Report Resource Website |
PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden (RRID:SCR_000615) | PRACSIS | material resource, biomaterial supply resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PRACSIS (Prognosis and Risk in Acute Coronary Syndromes In Sweden) aims to study prognosis and its predictors in a consecutive series of patients with acute coronary syndrome (ACS). The study is comprised of patients between 18 and 80 years diagnosed at the coronary care unit at the Sahlgrenska University Hospital with unstable angina, non-ST-elevation MI or ST-elevation MI. Extensive information on medical history and blood samples for analyses of biochemical markers and genetic factors have been collected. | cardiac disease, predictor, prognosis, medical history, biochemical marker, genetic factor, biomarker, gene, genetics, adult |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Karolisnka Biobank |
Acute coronary syndrome | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151442 | SCR_000615 | PRACSIS - Prognosis Risk in Acute Coronary Syndromes In Sweden, Prognosis and Risk in Acute Coronary Syndromes In Sweden, KI Biobank - PRACSIS | 2026-08-09 09:03:01 | 0 | ||||||
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NIH Toolbox Words-in Noise Test Resource Report Resource Website |
NIH Toolbox Words-in Noise Test (RRID:SCR_000174) | WIN Test | assessment test provider, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Assessment test that measures how much difficulty a person might have hearing in a noisy environment. A recorded voice instructs the participant to listen to and then repeat words. The task becomes increasingly difficult as the background noise gets louder. This test was developed to measure a person's ability to recognize single words presented amid varying levels of background noise. Recommended for participants ages 6-85 and takes approximately six minutes to administer. | sensation, audition, hearing, ear, noise | has parent organization: NIH Toolbox - Assessment of Neurological and Behavioral Function | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157784 | SCR_000174 | NIH Toolbox Words-in Noise (WIN) Test | 2026-08-09 09:02:55 | 0 | |||||||
|
Illuminate Resource Report Resource Website 1+ mentions |
Illuminate (RRID:SCR_000178) | Illuminate | software toolkit, software resource | Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically. | illumina, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02102 | SCR_000178 | Illuminate - Analytics toolkit for Illumina sequencer metrics | 2026-08-09 09:02:55 | 1 | |||||||
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NGS-Cleaner Resource Report Resource Website |
NGS-Cleaner (RRID:SCR_000574) | NGS-Cleaner | software application, software resource | Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01166 | SCR_000574 | 2026-08-09 09:03:00 | 0 | ||||||||
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Buss-Perry Aggression Questionnaire Resource Report Resource Website |
Buss-Perry Aggression Questionnaire (RRID:SCR_000177) | AGQ | assessment test provider, material resource | A 29 item aggression assessment where participants rank certain statements along a 5 point continuum from "extremely uncharacteristic of me"to "extremely characteristic of me". The scores are normalized on a scale of 0 to 1, with 1 being the highest level of aggression. The questionnaire returns scores for 4 dimensions of aggression: Physical Aggression, Verbal Aggression, Anger, Hostility. | psychology, scale, aggression, assessment, questionnaire, physical aggression, verbal aggression, anger, hostility | Physical Aggression, Verbal Aggression, Anger, Hostility | Public, Non-Commercial | nlx_157852 | SCR_000177 | Aggression Questionnaire, Buss Perry Aggression Questionnaire | 2026-08-09 09:02:55 | 0 | |||||||
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PEDIGREE-VISUALIZER Resource Report Resource Website |
PEDIGREE-VISUALIZER (RRID:SCR_000842) | PEDIGREE-VISUALIZER | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154521 | SCR_000842 | 2026-08-09 09:03:03 | 0 | |||||||||
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PEDPHASE Resource Report Resource Website |
PEDPHASE (RRID:SCR_000843) | PEDPHASE | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154525 | SCR_000843 | 2026-08-09 09:03:03 | 0 | ||||||||
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LOCUSMAP Resource Report Resource Website |
LOCUSMAP (RRID:SCR_000840) | LOCUSMAP | software application, software resource | Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 90/95, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154434, biotools:locusmap | https://bio.tools/locusmap | SCR_000840 | 2026-08-09 09:03:03 | 0 | ||||||||
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RHMAPPER Resource Report Resource Website |
RHMAPPER (RRID:SCR_000845) | RHMAPPER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154576 | SCR_000845 | 2026-08-09 09:03:03 | 0 | ||||||||
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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 | 2026-08-09 09:03:28 | 105 | ||||||
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Honey Bee Brain EST Project Resource Report Resource Website 1+ mentions |
Honey Bee Brain EST Project (RRID:SCR_002389) | Bee-ESTdb | material resource, biomaterial supply resource | A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu. | expressed sequence tag, brain, behavior, cdna, blast, gene, annotation, microarray, gene expression, comparative genomics, cdna clone, resource:genbank |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NSF ; University of Illinois Critical Research Initiatives Program ; Burroughs Wellcome Fund |
PMID:11932240 | Free | nif-0000-00118 | SCR_002389 | Honeybee EST Project | 2026-08-09 09:03:25 | 5 |
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