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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Lifelines Biobank Resource Report Resource Website 10+ mentions |
Lifelines Biobank (RRID:SCR_010730) | Lifelines Biobank | biomaterial supply resource, material resource | Overall aim of the LifeLines Study is to unravel the interaction between genetic and environmental factors in the development of multifactorial diseases, their concurrent development in individuals and their complications as a complex trait. The LifeLines database contains questionnaire data, physical measurements and biological samples from different health examinations. Collaboration is encouraged as it helps to maximize the scientific value of the wealth of epidemiologic data made possible by the participation of more than 165,000 individuals in the LifeLines Cohort Study. Primary objectives of the LifeLines Cohort Study are: a. Which are the disease overriding risk factors which predict the development of a multifactorial disease during lifetime? b. How are these universal risk factors modified, or what determines the effect of a universal risk factor in an individual? Specific research questions will focus on risk factors and modifiers (genetic, environmental and combined or complex factors) for single and multiple diseases. In addition to co-morbidity, LifeLines focuses on co-determinants. The primary endpoints include measures of aging, metabolic and endocrine diseases, cardiovascular and renal diseases, pulmonary and musculoskeletal diseases, and psychopathology. Secondary aims include the assessment of the prevalence and incidence of multifactorial diseases, their risk factors and their treatment in individuals as well as in families. The burden of disease for the society will be quantified in terms of care needed, and total costs of care. Until November 3, 2011, almost 68,000 subjects have been included in the study. The 60,000th participant was screened in the beginning of September 2011. Recruitment rate at present is between 700 and 800 subjects per week. The laboratory measurements which are performed has changed. As of October 2011, LifeLines will continue to measure: hematologic parameters, including hemoglobin, white blood cells, platelets, WBC differentiation, blood glucose, cholesterol, HDL-cholesterol, triglycerides, serum creatinin and sodium/potassium. Liver enzymes, thyroid hormones, calcium, phosphate, albumin, uric acid and microalbuminuria will not be measured routinely. The samples that are available for almost all participants, are: # serum (taken either with or without gel separator) # EDTA plasma # citrate plasma # DNA # early morning urine sample # urine samples of 24-hour urine collection Any researcher who is member of an internationally recognized academic institution and who is interested in utilizing the research possibilities, data and materials of LifeLines may apply for access. The applicant who is acting as Principal Investigator must be connected to a department or institution with the competence to carry out the research project to term. A contract will give the right to use the data for a pre-determined period of time. This contract also comprises the costs for the LifeLines Biobank which the investigator needs to reimburse. To apply for access, refer to the electronic application process. | blood, urine, plasma, serum, dna, edta plasma, citrate plasma, general population, clinical data, epidemiologic data, genetic factor, environmental factor, complex factor, multifactorial disease, risk factor, metabolic disease, endocrine disease, cardiovascular disease, renal disease, pulmonary disease, musculoskeletal disease, psychopathology, disease, nutrition, lifestyle, genetic epidemiology | is listed by: One Mind Biospecimen Bank Listing | General population, Aging | Public: Any researcher who is member of an internationally recognized academic institution and who is interested in utilizing the research possibilities, Data and materials of LifeLines may apply for access. A LifeLines Scientific Project is a project which uses data or results of biological examinations and measurements in materials from LifeLines (when both are used, The term LifeLines materials will be used). | nlx_93394 | SCR_010730 | LifeLines Cohort and Biobank, LifeLines Cohort Biobank, LifeLines Cohort & Biobank | 2026-08-15 11:29:58 | 30 | ||||||
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DWI/DTI Quality Control Tool: DTIPrep Resource Report Resource Website 1+ mentions |
DWI/DTI Quality Control Tool: DTIPrep (RRID:SCR_009562) | DTIPrep | software application, software resource | DTIPrep performs a Study-specific Protocol based automatic pipeline for DWI/DTI quality control and preparation. This is both a GUI and command line tool. The configurable pipeline includes image/diffusion information check, padding/Cropping of data, slice-wise, interlace-wise and gradient-wise intensity and motion check, head motion and Eddy current artifact correction, and DTI computing. | c++, linux, microsoft, magnetic resonance, nrrd, posix/unix-like, win32 (ms windows), windows, windows xp, dti | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155742 | http://www.nitrc.org/projects/dtiprep | SCR_009562 | 2026-08-15 11:29:47 | 4 | |||||||
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Paradigm Resource Report Resource Website 50+ mentions |
Paradigm (RRID:SCR_009634) | Paradigm | software resource | Software application for millisecond accurate experimental control for cognitive neuroscience, psychology and linguistics research. Presents text, images, sounds, movies, self-paced reading trials and rating scales. An integrated Python scripting API is available. Joystick and microphone response are available. Supports button boxes from PST, Cedrus, fORP and custom built response boxes. Paradigm can detect fMRI triggers through serial and parallel ports. Includes sample experiments that implement many of the most popular experiment designs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, experimental control, eye tracking, hardware, microsoft, magnetic resonance, physiological recording, python, scanner, win32 (ms windows), experiment, experimental design, fmri, eye tracking device | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155918 | SCR_009634 | Paradigm Experiment Builder | 2026-08-15 11:29:56 | 62 | |||||||
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Mach2dat Resource Report Resource Website 10+ mentions |
Mach2dat (RRID:SCR_009599) | software application, software resource | Software that performs logistic regression, using imputed SNP dosage data and adjusting for covariates. | genetic association, genomic analysis, imaging genomics, snp, gene, imputation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MACH 1.0 has parent organization: University of Michigan; Ann Arbor; USA |
PMID:21058334 PMID:19715440 |
Free, Non-commercial, Acknowledgement requested | nlx_155801 | http://www.nitrc.org/projects/mach2dat | SCR_009599 | Mach2dat: Association with MACH output | 2026-08-15 11:29:47 | 40 | ||||||
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FiberViewerLight Resource Report Resource Website 1+ mentions |
FiberViewerLight (RRID:SCR_009476) | FiberViewerLight | software application, software resource | Light version of the existing tool Fiber Viewer. It includes every clustering methods of Fiber Viewer such as : Lenght, Gravity, Hausdorff, and Mean methods but also a Normalized Cut algorithm. As in the full version you can also display a plane on the fiber. This tool works faster than the full version due to simplified visualizations. | c++, linux, microsoft, magnetic resonance, posix/unix-like | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155623 | SCR_009476 | 2026-08-15 11:29:46 | 5 | ||||||||
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MaCH-Admix Resource Report Resource Website 10+ mentions |
MaCH-Admix (RRID:SCR_009598) | software application, software resource | A genotype imputation software that is an extension to MaCH for faster and more flexible imputaiton, especially in admixed populations. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s). This reference selection method generates better imputation quality in shorter running time. MaCH-Admix also separates model parameter estimation from imputation. The separation allows users to perform imputation with standard reference panels + pre-calibrated parameters in a data independent fashion. Alternatively, if one works with study-specific reference panels, or isolated target population, one has the option to simultaneously estimate these model parameters while performing imputation. MaCH-Admix has included many other useful options and supports VCF input files. All existing MaCH documentation applies to MaCH-Admix. | genomic analysis, imaging genomics, imputation, snp, gene, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23074066 | Free, Non-commercial, Acknowledgement requested | nlx_155800, biotools:mach-admix | http://www.nitrc.org/projects/mach-admix, https://bio.tools/mach-admix | SCR_009598 | MaCH-Admix: Genotype Imputation Software | 2026-08-15 11:29:55 | 18 | ||||||
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Fiber-tracking based on Finsler distance Resource Report Resource Website 1+ mentions |
Fiber-tracking based on Finsler distance (RRID:SCR_009475) | Fiber-tracking based on Finsler distance | software application, software resource | Software provided as a sub-project in the Finsler-tractography module: http://www.nitrc.org/projects/finslertract | diffusion mr fiber tracking, fiber tracking, magnetic resonance, tractography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Finsler tractography module for Slicer |
3D Slicer License | nlx_155622 | SCR_009475 | 2026-08-15 11:29:57 | 1 | ||||||||
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False Discovery Rate Weighted Resource Report Resource Website 1+ mentions |
False Discovery Rate Weighted (RRID:SCR_009473) | False Discovery Rate Weighted | software application, software resource | Simple and efficient, this application performs the Weighted False Discovery Rate procedure of Benjamini and Hochberg (1997) to correct for multiple testing. The good think is that you can test virtually any number of p-values (even millions) obtained with any test-statistics for any data set. The bonus is that you can assign a-priori weights to give a better chance to those variables that you deem important. In practice, this procedure is powerful only with a relatively small number of p-values. | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155620 | SCR_009473 | 2026-08-15 11:29:46 | 1 | |||||||||
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Apache Hadoop Resource Report Resource Website 50+ mentions |
Apache Hadoop (RRID:SCR_011879) | Hadoop | software toolkit, software resource | Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets. | computing |
is listed by: OMICtools has parent organization: Apache Software Foundation |
Open unspecified license | OMICS_01210 | SCR_011879 | 2026-08-15 11:29:48 | 63 | ||||||||
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LDDMM Resource Report Resource Website 10+ mentions |
LDDMM (RRID:SCR_009590) | LDDMM | software application, software resource | Software application which aims to assign metric distances on the space of anatomical images in Computational Anatomy thereby allowing for the direct comparison and quantization of morphometric changes in shapes. As part of these efforts the Center for Imaging Science at Johns Hopkins University developed techniques to not only compare images, but also to visualize the changes and differences. For additional information please refer to: Faisal Beg, Michael Miller, Alain Trouve, and Laurent Younes. Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms. International Journal of Computer Vision, Volume 61, Issue 2; February 2005. M.I. Miller and A. Trouve and L. Younes, On the Metrics and Euler-Lagrange Equations of Computational Anatomy, Annual Review of biomedical Engineering, 4:375-405, 2002. Software developed with support from National Institutes of Health NCRR grant P41 RR15241. | analyze, c++, console (text based), linux, microsoft, magnetic resonance, posix/unix-like, shape analysis, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Johns Hopkins University; Maryland; USA |
nlx_155780 | http://www.nitrc.org/projects/lddmm-volume | SCR_009590 | Large Deformation Diffeomorphic Metric Mapping | 2026-08-15 11:29:47 | 31 | |||||||
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GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data Resource Report Resource Website 1+ mentions |
GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data (RRID:SCR_009581) | GMAC | software toolkit, software resource | Open-source software toolbox implemented multivariate spectral Granger Causality Analysis for studying brain connectivity using fMRI data. Available features are: fMRI data importing, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions are integrated into a graphical user interface developed in Matlab environment. Dependencies: Matlab, BIOSIG, SPM, MarsBar. | analyze, computational neuroscience, connectivity analysis, matlab, magnetic resonance, nifti, os independent, fmri, connectivity, granger causality, network analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Polytechnic University of Milan; Milan; Italy |
NIH Blueprint for Neuroscience Research | PMID:22925560 | nlx_155764 | http://www.nitrc.org/projects/gmac_2012 | http://selene.bioing.polimi.it/BBBlab/GMAC/ | SCR_009581 | Granger Multivariate Autoregressive Connectivity | 2026-08-15 11:29:55 | 1 | ||||
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TAGGER Resource Report Resource Website 50+ mentions |
TAGGER (RRID:SCR_009419) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, web-based |
is listed by: Genetic Analysis Software is listed by: SoftCite |
nlx_154669 | SCR_009419 | 2026-08-15 11:29:56 | 93 | ||||||||||
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SPLINK Resource Report Resource Website 10+ mentions |
SPLINK (RRID:SCR_009414) | software application, software resource | Software application for linkage analysis using affected sib pairs (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, sunos, ms-dos | is listed by: Genetic Analysis Software | nlx_154659 | http://www-gene.cimr.cam.ac.uk/clayton/software/ | SCR_009414 | affected Sib Pairs LINKage analysis | 2026-08-15 11:29:54 | 49 | ||||||||
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SSAHASNP Resource Report Resource Website 1+ mentions |
SSAHASNP (RRID:SCR_009415) | SSAHASNP | software application, software resource | A polymorphism detection tool that detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. For those less repetitive or non-repetitive reads, we place them uniquely on the reference genome sequence and find the best alignment according to the pair-wise alignment score if there are multiple seeded regions. From the best alignment, SNP candidates are screened, taking into account the quality value of the bases with variation as well as the quality values in the neighbouring bases, using neighbourhood quality standard (NQS). For insertions/deletions, we check if the same indel is mapped by more than one read, ensuring the detected indel with high confidence. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154661 | SCR_009415 | Sequence Search and Alignment by Hashing Algorithm for SNP detection | 2026-08-15 11:29:46 | 4 | ||||||||
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BrainGraph Editor Resource Report Resource Website 1+ mentions |
BrainGraph Editor (RRID:SCR_009536) | BrainGraph Editor | software application, software resource | A JAVA application designed to create taxonomies or hierarchies in order to classify and organize information. | gnome, information resource, information specification, java, kde, ontology, os independent, visualization, win32 (ms windows), taxonomy, hierarchy, classify, organize |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Laboratory of Neuro Imaging |
BIRN License, LONI Software License | nlx_155713 | http://www.nitrc.org/projects/braingrpheditor | SCR_009536 | 2026-08-15 11:29:57 | 3 | |||||||
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SPIP Resource Report Resource Website 100+ mentions |
SPIP (RRID:SCR_009410) | software application, software resource | Software application that simulate pedigrees and genetic data in age-structured populations (entry from Genetic Analysis Software) | gene, genetic, genomic, c | is listed by: Genetic Analysis Software | nlx_154657 | SCR_009410 | Simulate Pedigree In Population | 2026-08-15 11:29:54 | 433 | |||||||||
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SPLAT Resource Report Resource Website 10+ mentions |
SPLAT (RRID:SCR_009411) | SPLAT | software application, software resource | Software application that can calculate virtually any linkage test statistic under several sib pair study designs: affected, discordant, unaffected, and pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. It uses the EM algorithm to compute maximum likelihood estimates of sharing (subject to any user-specified domain restrictions or null hypotheses) and then plots lod scores versus chromosomal position. It includes a novel grid scanning capability that enables simultaneous visualization of multiple test statistics. Phenotype definitions can be modified without recalculating inheritance vectors, thereby providing considerable analytical flexibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, qt, unix, sunos, linux, macos, ms-windows, (2000/xp) | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154658 | SCR_009411 | Sib Pair Linkage Analysis Testing | 2026-08-15 11:29:56 | 19 | |||||||
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PLABQTL Resource Report Resource Website 10+ mentions |
PLABQTL (RRID:SCR_012789) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154535 | SCR_012789 | PLAnt Breeding QTL analysis | 2026-08-15 11:29:56 | 14 | |||||||||
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Texas Human Biologics Resource Report Resource Website 1+ mentions |
Texas Human Biologics (RRID:SCR_010523) | biomaterial supply resource, material resource | Biotechnology company dedicated to enhancing quality of patient care through development and manufacture of safe, high quality allograft solutions for healthcare professionals. | works with: Bone Bank Allografts | nlx_20452 | SCR_010523 | 2026-08-15 11:29:58 | 6 | |||||||||||
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HAPBLOCK 2 Resource Report Resource Website |
HAPBLOCK 2 (RRID:SCR_012788) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, stata | is listed by: Genetic Analysis Software | nlx_154376 | SCR_012788 | 2026-08-15 11:29:58 | 0 |
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