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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
pyxnat Resource Report Resource Website 1+ mentions |
pyxnat (RRID:SCR_002574) | pyxnat | software toolkit, software resource, software library | Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data. | computed tomography, magnetic resonance, pet, spect, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: XNAT - The Extensible Neuroimaging Archive Toolkit |
European Union | PMID:22654752 | Free, Available for download, Freely available | nlx_155977 | https://sources.debian.org/src/python-pyxnat/ | SCR_002574 | pyxnat: XNAT in Python | 2026-08-15 11:22:15 | 1 | ||||
|
NIPY Resource Report Resource Website 10+ mentions |
NIPY (RRID:SCR_002489) | NIPY | software toolkit, image analysis software, data processing software, software application, software resource, software library | A complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI). | magnetic resonance, python, neuroimaging, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
Free, Available for download, Freely available | nlx_155883 | http://www.nitrc.org/projects/nipy | SCR_002489 | NIPY Structural and Functional Analysis | 2026-08-15 11:22:14 | 33 | ||||||
|
Presentation Resource Report Resource Website 1000+ mentions |
Presentation (RRID:SCR_002521) | Presentation | data processing software, software application, data analysis software, software resource | Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures. | stimulus delivery, event logging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download | nlx_155925 | http://www.nitrc.org/projects/presentation | SCR_002521 | Presentation 19.0 | 2026-08-15 11:22:13 | 1570 | ||||||
|
Stowers Original Data Repository Resource Report Resource Website 10+ mentions |
Stowers Original Data Repository (RRID:SCR_002640) | Stowers ODR, ODR | database, bibliography, data repository, storage service resource, data or information resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Open access repository of original, unprocessed data underlying work published by Stowers researchers to allow the scientific community to validate and extend the findings made by Stowers researchers. For papers first submitted for publication after November 1, 2011, the Stowers Institute requires its members to deposit original data files into the Stowers Original Data Repository or to repositories maintained by third parties at the time of publication. Access to the Stowers Original Data Repository is free, but you will be asked to register before you can download data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data set, image |
is related to: OME-TIFF Format has parent organization: Stowers Institute for Medical Research |
Free, Available for download, Freely available | nlx_156067 | SCR_002640 | Stowers Institute Original Data Repository | 2026-08-15 11:22:14 | 12 | |||||||
|
University of Arkansas; Arkansas; USA Resource Report Resource Website 1+ mentions |
University of Arkansas; Arkansas; USA (RRID:SCR_002515) | UARK, UA | university | Public, co educational research university in Fayetteville, Arkansas. | public research university, coeducational university |
is related to: University of Arkansas MicroCT Imaging Consortium for Research and Outreach is parent organization of: Neuroscience Course - Atlas Images is parent organization of: BciPep is parent organization of: University of Arkansas Stable Isotope Lab Core Facility is parent organization of: University of Arkansas Labs and Facilities is parent organization of: University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility is parent organization of: University of Arkansas AIMRC Imaging and Spectroscopy Core Facility is parent organization of: University of Arkansas AIMRC Bioenergetics Core Facility is parent organization of: University of Arkansas AIMRC Data Science Core Facility |
Free | ISNI:0000 0001 2151 0999, grid.411017.2, Wikidata:Q1070333, Crossref funder ID:100007756, nlx_90713 | https://ror.org/05jbt9m15 | SCR_002515 | University of Arkansas, UArkansas | 2026-08-15 11:22:12 | 2 | ||||||
|
ParaView Resource Report Resource Website 500+ mentions |
ParaView (RRID:SCR_002516) | ParaView | data processing software, software application, data analysis software, software resource, data visualization software | Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data. | magnetic resonance |
uses: VTK is used by: Spine Detection and Extraction is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SIGEN has parent organization: Kitware |
Free, Available for download, Freely available | nlx_155917 | http://www.nitrc.org/projects/paraview, https://sources.debian.org/src/paraview/ | SCR_002516 | 2026-08-15 11:22:15 | 685 | |||||||
|
Spatial Statistical Parametric Mapping Resource Report Resource Website 1+ mentions |
Spatial Statistical Parametric Mapping (RRID:SCR_002592) | SSPM | image analysis software, image processing software, data processing software, software application, software resource | Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies. | imaging genomics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is parent organization of: Functional Analysis of Diffusion Tensor |
Free, Available for download, Freely available | nlx_155996 | SCR_002592 | 2026-08-15 11:22:16 | 1 | ||||||||
|
ORS Visual SI Resource Report Resource Website 1+ mentions |
ORS Visual SI (RRID:SCR_002509) | ORS Visual SI | commercial organization, data processing software, software application, software resource, data visualization software | Software with advanced visualization techniques and state-of-the-art volume rendering provide unparalleled insight into the details and properties of neurological data acquired by CT, micro-CT, MRI, PET, SPECT, microscopy and other modalities. With data fusion tools, intramodality and multimodality registration of MR/CT or PET/CT is easily accomplished, while semi-automatic VOI delineation on fused datasets can improve analysis. Standard formats, such as DICOM, RAW, JPEG, NIFTI, Analyze are supported and 3D/4D sequences can be played. Other features include MPR, oblique, CPR, volume clipping, and surface visualization of cortex, skull, and scalp models. Also standard are easy-to-use tools for voxel-based delineation of features and the measurement of properties, including areas, volumes, counts, and intensity profiles. Present your findings by creating annotated animations or high-resolution images for posters. An SDK is also available to create plug-ins that provide new workflows or functionalities. | active contour, animation, clipping, computed tomography, image display, image reconstruction, magnetic resonance, optical imaging, pet, spect, quantification, quantitative shape analysis, region growing, region of interest, rendering, segmentation, shape analysis, surface analysis, surface rendering, three dimensional display, two dimensional display, visualization, vitual endoscopy, volume measurement, volume rendering, volumetric analysis, english, french, italian, japanese, portuguese, spanish | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155908 | http://www.nitrc.org/projects/orsvisual_si | SCR_002509 | Object Research Systems Visual SI | 2026-08-15 11:22:12 | 1 | ||||||
|
RUbioSeq Resource Report Resource Website 10+ mentions |
RUbioSeq (RRID:SCR_002508) | standalone software, data processing software, software application, data analysis software, software resource, sequence analysis software | Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments. | resequencing analysis, exome variant detection, pipeline, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
BLUEPRINT Consortium FP7/2007-2013 282510; Spanish Ministry of Economy and Competitiveness BIO2007-666855 |
PMID:23630175 | Free, Available for download | biotools:rubioseq, OMICS_00072 | https://sourceforge.net/projects/rubioseq/files/, https://bio.tools/rubioseq | SCR_002508 | RUbioSeq+ | 2026-08-15 11:22:16 | 12 | |||||
|
OMERO Resource Report Resource Website 100+ mentions |
OMERO (RRID:SCR_002629) | OMERO | image analysis software, data management software, data processing software, software application, software resource, data visualization software | Client-server software for management, visualization, and analysis of biological microscopy images. OMERO handles images in a secure central repository where users can view, organize, analyze and share data from anywhere with internet access. Work with images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. | light microscopy, electron microscopy, genotype, archiving, data repository, data sharing, image, metadata |
is listed by: FORCE11 is related to: Bio-Formats has parent organization: OME - Open Microscopy Environment |
BBSRC BB/G022585; BBSRC BB/I000755; BBSRC BB/G022577; Jisc REXDAT03 |
PMID:22373911 | Free, Available for download, Freely available | nlx_156069 | SCR_002629 | OMERO - Open Microscopy Environment Remote Objects, Open Microscopy Environment Remote Objects, OME Remote Objects | 2026-08-15 11:22:17 | 190 | |||||
|
Normative Independent Component Analysis Resource Report Resource Website 1+ mentions |
Normative Independent Component Analysis (RRID:SCR_002506) | NICA | data processing software, software application, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99. | eeg, meg, electrocorticography, fourier time-domain analysis, independent component analysis, spectral analysis, statistical operation, temporal transformation, blind source separation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | PMID:20598764 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155906 | http://www.nitrc.org/projects/nica | SCR_002506 | 2026-08-15 11:22:12 | 5 | ||||||
|
wateRmelon Resource Report Resource Website 100+ mentions |
wateRmelon (RRID:SCR_001296) | wateRmelon | software resource | Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages. | dna methylation, microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23631413 | Free, Available for download, Freely available | OMICS_02039, biotools:watermelon | https://bio.tools/watermelon | SCR_001296 | 2026-08-15 11:21:55 | 314 | ||||||
|
NGSrich Resource Report Resource Website 10+ mentions |
NGSrich (RRID:SCR_001333) | software resource | Software for target enrichment performance for next-generation sequencing. | standalone software, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22290614 | Free, Available for download, Freely available | OMICS_03603, biotools:ngsrich | https://bio.tools/ngsrich | SCR_001333 | 2026-08-15 11:21:56 | 10 | |||||||
|
oneChannelGUI Resource Report Resource Website 10+ mentions |
oneChannelGUI (RRID:SCR_001325) | oneChannelGUI | software resource | Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, rna-seq, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:17875544 | Free, Available for download, Freely available | biotools:onechannelgu, OMICS_02004 | http://www.bioconductor.org/packages/release/bioc/html/oneChannelGUI.html | SCR_001325 | 2026-08-15 11:22:04 | 13 | ||||||
|
CYCLE Resource Report Resource Website 1+ mentions |
CYCLE (RRID:SCR_001328) | CYCLE | software resource | Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models. | r, microarray, time course, periodic expression pattern, time-series, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18310054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02010, biotools:cycle | http://www.bioconductor.org/packages/release/bioc/html/cycle.html, https://bio.tools/cycle | SCR_001328 | 2026-08-15 11:22:04 | 4 | ||||||
|
LMGene Resource Report Resource Website 1+ mentions |
LMGene (RRID:SCR_001329) | LMGene | software resource | Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays. | differential expression, microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02009 | http://www.bioconductor.org/packages/release/bioc/html/LMGene.html | SCR_001329 | 2026-08-15 11:21:55 | 4 | |||||||
|
affylmGUI Resource Report Resource Website 10+ mentions |
affylmGUI (RRID:SCR_001320) | affylmGUI | software resource | R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11. | affymetrix, differential expression, r, data import, differential expression, gui, microarray, multiple comparison, one channel, preprocessing, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia has parent organization: Bioconductor |
PMID:16455752 | Free, Available for download, Freely available | biotools:affylmgui, OMICS_02016 | http://www.bioconductor.org/packages/release/bioc/html/affylmGUI.html, https://bio.tools/affylmgui | SCR_001320 | Affymetrix linear modeling Graphical User Interface | 2026-08-15 11:21:55 | 31 | |||||
|
arrayQuality Resource Report Resource Website 1+ mentions |
arrayQuality (RRID:SCR_001315) | arrayQuality | software resource | Software functions for performing print-run and array level quality assessment. | microarray, quality control, two channel, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU Lesser General Public License | OMICS_02020 | SCR_001315 | arrayQuality - Assessing array quality on spotted arrays | 2026-08-15 11:22:04 | 8 | |||||||
|
ArrayTools Resource Report Resource Website 50+ mentions |
ArrayTools (RRID:SCR_001313) | ArrayTools | software resource | Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases. | annotation, differential expression, microarray, one channel, preprocessing, quality control, report writing, statistical method, visualization, FASEB list |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02022 | http://www.bioconductor.org/packages/release/bioc/html/ArrayTools.html | SCR_001313 | ArrayTools - GeneChip Analysis Package | 2026-08-15 11:21:55 | 94 | ||||||
|
affyPLM Resource Report Resource Website 100+ mentions |
affyPLM (RRID:SCR_001319) | affyPLM | software resource | Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools. | microarray, one channel, preprocessing, quality control |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02017 | SCR_001319 | affyPLM - Methods for fitting probe-level models | 2026-08-15 11:22:04 | 163 |
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.
