Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Social Deprivation Index Resource Report Resource Website 10+ mentions |
Social Deprivation Index (RRID:SCR_025026) | SDI | data or information resource, portal | SDI is composite measure of area level deprivation based on seven demographic characteristics collected in the American Community Survey and used to quantify the socio-economic variation in health outcomes. | American Community Survey, demographic characteristics, quantify socio-economic variation in health outcomes, | Free, Freely available | SCR_025026 | 2026-08-12 10:53:22 | 14 | ||||||||||
|
moseq2-app Resource Report Resource Website |
moseq2-app (RRID:SCR_025031) | software resource, source code | Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time. | OpenBehavior, Motion Sequencing, describe mouse behavior, depth camera, extract mouse pose, extract mouse pose from depth video, depth video, pose evolve over time, | has parent organization: Harvard University; Cambridge; United States | Free, Available for download, Freely available | SCR_025031 | MoSeq2 Jupyter Notebook platform, moseq2-app | 2026-08-12 10:53:22 | 0 | |||||||||
|
BayCEST Resource Report Resource Website |
BayCEST (RRID:SCR_024951) | software resource, software application | Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra. | Bayesian analysis, chemical exchange saturation transfer, z-spectra, | is listed by: FSL | Free, Freely available | SCR_024951 | Bayesian Chemical Exchange Saturation Transfer | 2026-08-12 10:53:15 | 0 | |||||||||
|
PMI Resource Report Resource Website 1+ mentions |
PMI (RRID:SCR_025084) | software resource, source code | Software tool to support translation of basic research in medical image analysis into early clinical studies. | medical image analysis, clinical studies, | Free, Available for download, Freely available | https://github.com/plaresmedima/PMI-0.4 | SCR_025084 | PMI 0.4, Platform for Research in Medical Imaging | 2026-08-12 10:53:19 | 1 | |||||||||
|
Fslutils Resource Report Resource Website 1+ mentions |
Fslutils (RRID:SCR_024943) | data processing software, software resource, software application | Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets. | FSL, conversion, processing, Analyze format data sets, Nifti format data sets, | is a plug in for: FSL | Free, Freely available, | SCR_024943 | FSLUTILS | 2026-08-12 10:53:21 | 7 | |||||||||
|
Atlasquery Resource Report Resource Website 1+ mentions |
Atlasquery (RRID:SCR_024944) | software resource, software application | Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask. | FSL, atlas images, command line interrogation, FSL atlases, | is a plug in for: FSL | Free, Freely available | SCR_024944 | 2026-08-12 10:53:16 | 1 | ||||||||||
|
GROMACS topology editors Resource Report Resource Website 1+ mentions |
GROMACS topology editors (RRID:SCR_025013) | gmxtras | software resource, software application | Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files. | GROMACS, topology files, force fields, modify GROMACS topology files, | Free, Available for download, Freely available | SCR_025013 | 2026-08-12 10:53:16 | 2 | ||||||||||
|
ICA-PNM Resource Report Resource Website |
ICA-PNM (RRID:SCR_024952) | data processing software, software resource, software application | Software de-noising pipeline combines noise regressors identified by tools such as PNM and ICA (and FIX) and effectively prepares them for entry into single FEAT model, thus allowing the user to clean data in single step. | clean data, de-noising, clean data in single step, | is listed by: FSL | Free, Freely available | SCR_024952 | 2026-08-12 10:53:21 | 0 | ||||||||||
|
Genotype Sparse Compression Resource Report Resource Website 1+ mentions |
Genotype Sparse Compression (RRID:SCR_025071) | GSC | software resource, software application | Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities. | lossless compression of VCF files, store and manage VCF files, compressed format, | SCR_025071 | Genotype Sparse Compression (GSC) | 2026-08-12 10:53:23 | 1 | ||||||||||
|
fsl-cluster Resource Report Resource Website |
fsl-cluster (RRID:SCR_024938) | software resource, software application | Software application used to form clusters, report information about clusters and/or perform cluster based inference. | FSL, form clusters, report information about clusters, perform cluster based inference, | is a plug in for: FSL | Free, Freely available | SCR_024938 | cluster | 2026-08-12 10:53:21 | 0 | |||||||||
|
XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software resource, software application | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-08-12 10:53:16 | 4 | ||||||||
|
eddy Resource Report Resource Website 1+ mentions |
eddy (RRID:SCR_024934) | data processing software, software resource, software application | Software tool for correcting eddy currents and movements in diffusion data. Used to predict undistorted data, to which actual observed images can be aligned, to estimate and to correct for volume-to-volume movement and off-resonance fields, to signal dropout caused by movement during diffusion encoding, within-volume movement and movement-induced changes of susceptibility-induced off-resonance field. In addition to correcting for these effects, the output from this framework offers description of off resonance and subject movement effects present in uncorrected data. | correcting eddy currents and movements, diffusion data correction, | is a plug in for: FSL | Free, Freely available | SCR_024934 | 2026-08-12 10:53:14 | 9 | ||||||||||
|
randomise Resource Report Resource Website 10+ mentions |
randomise (RRID:SCR_024937) | software resource, software application | Software tool for nonparametric permutation inference on neuroimaging data. | nonparametric permutation inference, neuroimaging data | is a plug in for: FSL | PMID:24530839 | Free, Freely available | SCR_024937 | 2026-08-12 10:53:14 | 12 | |||||||||
|
snm3C Pipeline Resource Report Resource Website 1+ mentions |
snm3C Pipeline (RRID:SCR_025041) | snM3C | data processing software, software resource, software application | Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics. | data processing, single-nucleus methylome data, single-cell data, chromatin contact data, single-cell methylome and chromatin contact sequencing data, |
is organization facet of: BICCN is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Freely available | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/snM3C | SCR_025041 | , Single Nucleus Methly-Seq and Chromatin Capture, single-nucleus Methylome and Chromatin Contact, Single Nucleus Methly-Seq and Chromatin Capture (snM3C) | 2026-08-12 10:53:22 | 2 | |||||||
|
Numba Resource Report Resource Website 1+ mentions |
Numba (RRID:SCR_025056) | software resource, software application | Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks. | Accelerate Python functions, JIT compiler, translate subset of Python and NumPy code into fast machine code, | Anaconda ; Inc. |
Free, Available for download, Freely available, | https://numba.pydata.org, https://github.com/numba/numba/blob/c6da26929c7fc18b06dd2e5fc86982cea828df6c/docs/source/index.rst | SCR_025056 | 2026-08-12 10:53:23 | 8 | |||||||||
|
LDbase Resource Report Resource Website |
LDbase (RRID:SCR_025052) | service resource, data repository, storage service resource | NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities. | behavioral project oriented data, learning disabilities, | has parent organization: Florida State University; Florida; USA | NICHD R01HD095193 | Free, Freely available | r3d100014160 | https://doi.org/10.17616/R31NJNF4 | SCR_025052 | Learning and Development data repository | 2026-08-12 10:53:22 | 0 | ||||||
|
Abaqus FEA Resource Report Resource Website 10+ mentions |
Abaqus FEA (RRID:SCR_024997) | software resource, software application | Software suite for finite element analysis and computer aided engineering. | Simulia, finite element analysis, computer aided engineering, | Restricted | https://en.wikipedia.org/wiki/Abaqus | SCR_024997 | Simulia Abaqus FEA | 2026-08-12 10:53:22 | 28 | |||||||||
|
OutLyzer Resource Report Resource Website 1+ mentions |
OutLyzer (RRID:SCR_025120) | software resource, source code | Software tool for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Detects variations, specifically low allele frequency variation, in next generation sequencing data. | Detects variations, variant caller, low allele frequency variation, extracting low-allele-frequency tumor mutations, next generation sequencing data | Institut National du Cancer | PMID:27825131 | Free, Available for download, Freely available | https://github.com/EtieM/outLyzer | SCR_025120 | 2026-08-12 10:53:19 | 1 | ||||||||
|
Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | data or information resource, atlas, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | NSERC Discovery ; NCCIH U41 AT008718; NIGMS R01 GM125943; NCCIH F31 AT010098; NCI F31 CA236237; NCCIH T32 AT007533; NIH D43 TW010530; NSF ; BBSRC ; Carnegie Trust for the Universities of Scotland ; Netherlands eScience Center ; Sao Paulo Research Foundation ; NCCIH AT008718; NIGMS GM124461; Natural Sciences and Engineering Research Council of Canada ; Ministry of Science ; Technology and Telecommunications of Costa Rica |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-08-12 10:53:18 | 36 | ||||||
|
JaCoP Resource Report Resource Website 10+ mentions |
JaCoP (RRID:SCR_025164) | JaCoP | software toolkit, software resource, source code | Software toolbox as plugin for ImageJ that supports colocalization analysis in light microscopy. Used for subcellular colocalization analysis under ImageJ that integrates current global statistic methods and novel object-based approach. | ImageJ, subcellular colocalization analysis, colocalization analysis, | is a plug in for: ImageJ | PMID:17210054 | Free, Available for download, Freely available | SCR_025164 | Just Another Colocalization Plugin | 2026-08-12 10:53:24 | 37 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
