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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Statistical non-Parametric Mapping Resource Report Resource Website 50+ mentions |
Statistical non-Parametric Mapping (RRID:SCR_002092) | SnPM | data processing software, software application, software resource, software toolkit | A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM. | analyze, linear, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, regression, statistical operation, sunos/solaris, windows, statistical parametric mapping, pet, spect |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: SPM has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Warwick; Coventry; United Kingdom |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00342 | http://www.nitrc.org/projects/snpm | SCR_002092 | SnPM: Statistical nonParametric Mapping, SnPM - Statistical NonParametric Mapping - A toolbox for SPM, Statistical nonParametric Mapping | 2026-09-12 01:00:53 | 95 | |||||
|
Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software resource, software toolkit | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene, https://sources.debian.org/src/ugene/ | SCR_005579 | 2026-09-12 01:02:34 | 183 | ||||||
|
Publish or perish Resource Report Resource Website 1+ mentions |
Publish or perish (RRID:SCR_005968) | PoP | software application, software resource | Software program that allows researchers to perform citation analysis and calculate various impact metrics. It uses Google Scholar to obtain the raw citations, then analyzes these and presents the following statistics: * Total number of papers * Total number of citations * Average number of citations per paper * Average number of citations per author * Average number of papers per author * Average number of citations per year * Hirsch''s h-index and related parameters * Egghe''s g-index * The contemporary h-index * The age-weighted citation rate * Two variations of individual h-indices * An analysis of the number of authors per paper. The results are available on-screen and can also be copied to the Windows clipboard (for pasting into other applications) or saved to a variety of output formats (for future reference or further analysis). The Publish or Perish software is a Microsoft Windows application that can also be installed and used on Apple Mac OS X and GNU/Linux computers, with the aid of a suitable emulator such as Wine or CrossOver Mac. | impact factor, altmetrics, citation analysis, metrics, windows | is listed by: FORCE11 | Acknowledgement requested | nlx_151328 | SCR_005968 | 2026-09-12 01:02:35 | 8 | ||||||||
|
Samba Resource Report Resource Website 100+ mentions |
Samba (RRID:SCR_006557) | Samba | software application, software resource, systems interoperability software | Standard Windows interoperability suite of programs for Linux and Unix that provides secure, stable and fast file and print services for all clients using the SMB/CIFS protocol, such as all versions of DOS and Windows, OS/2, Linux and many others. Samba is an important component to seamlessly integrate Linux/Unix Servers and Desktops into Active Directory environments using the winbind daemon. | interoperability, linux, unix, windows | is parent organization of: rsync | GNU General Public License | nlx_156712 | SCR_006557 | 2026-09-12 01:02:36 | 133 | ||||||||
|
REAPER Resource Report Resource Website 10+ mentions |
REAPER (RRID:SCR_009354) | REAPER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Tag SNP selection tool according to r2-bins method that is specifically designed for full genome scale deterministic tagging. | gene, genetic, genomic, windows, linux |
is listed by: Genetic Analysis Software has parent organization: University of Tartu; Tartu; Estonia |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154569 | SCR_009354 | 2026-09-12 01:02:45 | 11 | ||||||||
|
E-Prime Resource Report Resource Website 100+ mentions |
E-Prime (RRID:SCR_009567) | E-Prime | software application, software resource | A suite of applications to fulfill all of your computerized experiment needs. Used by more than 15,000 professionals in the research community, E-Prime provides a truly easy-to-use environment for computerized experiment design, data collection, and analysis. E-Prime provides millisecond precision timing to ensure the accuracy of your data. E-Prime's flexibility to create simple to complex experiments is ideal for both novice and advanced users. The E-Prime suite of applications includes: * E-Studio ? Drag and drop graphical interface for experiment design * E-Basic ? Underlying scripting language of E-Prime * E-Run ? Once the experiment is generated with a single click, E-Run affords you the millisecond precision of stimulus presentation, synchronizations, and data collection. * E-Merge ? Merges your single session data files for group analysis * E-DataAid ? Data management utility * E-Recovery ? Recovers data files | experimental control, microsoft, magnetic resonance, visual basic, win32 (ms windows), windows, windows vista, windows xp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite |
nlx_155747 | http://www.nitrc.org/projects/eprime | SCR_009567 | E-Prime 2.0 | 2026-09-12 01:02:47 | 173 | |||||||
|
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 | 2026-09-12 01:02:46 | 4 | |||||||
|
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 | 2026-09-12 01:02:47 | 31 | |||||||
|
Solar Eclipse Imaging Genetics tools Resource Report Resource Website 10+ mentions |
Solar Eclipse Imaging Genetics tools (RRID:SCR_009645) | Solar Eclipse Imaging Genetics tools | software application, software resource | Software tools optimized for performing univariate and multivariate imaging genetics analyses while providing practical correction strategies for multiple testing. The goal of this project is to merge two important research directions in modern science, genetics and neuroimaging. This entails combining modern statistical genetic methods and quantitative phenotyping performed with high dimensional neuroimaging modalities. So far, however, standard imaging tools are unable to deal with large-scale genetics data, and standard genetics tools, in turn, are unable to accommodate large size and binary format of the image data. Their focus is to create imaging genetics tools for classical genetic and epigenetic epidemiological analyses such as heritability, pleiotropy, quantitative trait loci (QTL) and genome-wide association (GWAS), gene expression, and methylation analyses optimized for traits derived from structural and functional brain imaging data | c++, genetic association, genomic analysis, gifti, imaging genomics, linux, loni pipeline, macos, microsoft, nifti, posix/unix-like, snp, gene, windows, windows xp, genetics, neuroimaging, heritability, pleiotropy, quantitative trait loci, genome-wide association, gene expression, methylation, trait, structural neuroimaging, functionalneuroimaging, brain imaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Non-commercial, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552 | nlx_155966 | SCR_009645 | 2026-09-12 01:02:47 | 14 | ||||||||
|
Brain Decoder Toolbox Resource Report Resource Website 1+ mentions |
Brain Decoder Toolbox (RRID:SCR_013150) | BDTB | software application, software resource | Software that performs ?decoding? of brain activity, by learning the difference between brain activity patterns among conditions and then classifying the brain activity based on the learning results. BDTB is a set of Matlab functions. BDTB is OS-independent. | analyze, japanese, linux, macos, matlab, microsoft, magnetic resonance, posix/unix-like, windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
PMID:15852014 | GNU General Public Licence | nlx_155709 | http://www.nitrc.org/projects/bdtb | SCR_013150 | BrainDecoderToolbox | 2026-09-12 01:02:48 | 2 | |||||
|
Clinical Trial Management Application Resource Report Resource Website |
Clinical Trial Management Application (RRID:SCR_013531) | CTMA | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 11, 2012. The Clinical Trials Management Tools are Java-based suite (accessed via a secure intranet) for managing various aspects of a clinical trial, research protocols, outcomes initiatives, statistical research analysis, as well as CTEP/CDUS reporting. Developed in collaboration with the Clinical Research Services (CRS) Office at the UPCI, this research-based application provides an integrated tool for managing administrative (e.g. IRB submissions and approvals) and clinical (e.g. tumor measurements, registrations/ screenings) functions for the collection and analysis of data generated from a clinical trial. More information can be found here, http://www.upci.upmc.edu/spore/skin/coreD.cfm | clinical trial, clinical, research protocol, outcomes initiative, statistical research analysis, ctep reporting, cdus reporting, clinical study, bioinformatics, computer platform, windows |
is listed by: Biositemaps has parent organization: University of Pittsburgh; Pennsylvania; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33266 | SCR_013531 | Clinical Trial Management Application (CTMA) | 2026-09-12 01:02:49 | 0 | |||||||
|
BD FACSDiva Software Resource Report Resource Website 5000+ mentions |
BD FACSDiva Software (RRID:SCR_001456) | BD FACSDiva Software | commercial organization, software resource | A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories. | flow cytometry, windows |
is used by: BD Biosciences: LSRFortessa X-20 Cell Analyzer has parent organization: BD Biosciences |
Free, Freely Available | SciRes_000115 | http://www.bdbiosciences.com/instruments/software/facsdiva/index.jsp | SCR_001456 | 2026-09-12 01:03:11 | 8327 | |||||||
|
CodonCodes TraceViewer Resource Report Resource Website 1+ mentions |
CodonCodes TraceViewer (RRID:SCR_002304) | TraceViewer | commercial organization, software resource | A Java program that allows you to see, print, and edit DNA sequencing traces. | windows, dna sequencing trace, dna, sequencing, trace | is listed by: OMICtools | Free for academic use | OMICS_01822 | SCR_002304 | CodonCode''s TraceViewer | 2026-09-12 01:03:12 | 1 | |||||||
|
Visual Molecular Dynamics Resource Report Resource Website 100+ mentions |
Visual Molecular Dynamics (RRID:SCR_001820) | VMD | software resource, source code | A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. | standalone software, mac os x, unix, virtual machine, windows, c++ |
is listed by: OMICtools has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NIGMS | PMID:8744570 | Free, Freely available | OMICS_03804 | SCR_001820 | 2026-09-12 01:03:12 | 383 | ||||||
|
BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | software resource, source code | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-09-12 01:03:14 | 21 | ||||||
|
SigmaPlot Resource Report Resource Website 10000+ mentions |
SigmaPlot (RRID:SCR_003210) | SigmaPlot | commercial organization, software resource | Statistical analysis and scientific graphing software for Windows OS. | statistics, windows, graph, data analysis | is listed by: SoftCite | Commercial license | SciRes_000184 | SCR_003210 | sigma plot | 2026-09-12 01:03:13 | 17386 | |||||||
|
MCMC.qpcr Resource Report Resource Website 10+ mentions |
MCMC.qpcr (RRID:SCR_001721) | software resource | Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977043 | Free, Available for download, Freely available | OMICS_03934 | SCR_001721 | MCMC.qpcr: Bayesian analysis of qRT-PCR data | 2026-09-12 12:55:30 | 24 | |||||||
|
plateCore Resource Report Resource Website |
plateCore (RRID:SCR_001743) | data or information resource, database, software resource | Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956418 | Free, Available for download, Freely available | OMICS_05641 | http://www.bioconductor.org/packages/release/bioc/html/plateCore.html | SCR_001743 | plateCore - Statistical tools and data structures for plate-based flow cytometry | 2026-09-12 12:55:30 | 0 | ||||||
|
SLqPCR Resource Report Resource Website 10+ mentions |
SLqPCR (RRID:SCR_001669) | software resource | Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH. | standalone software, mac os x, unix/linux, windows, r, microtitre plate assay, qpcr |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_04010 | SCR_001669 | SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH | 2026-09-12 12:55:29 | 25 | ||||||||
|
NASTIseq Resource Report Resource Website 1+ mentions |
NASTIseq (RRID:SCR_001797) | NASTIseq | software resource | Software for integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. | r, antisense transcript, rna, antisense, transcript, linux, windows, strand-specific rna sequencing, cis-natural antisense transcript |
is listed by: OMICtools has parent organization: Duke University; North Carolina; USA |
PMID:23816784 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01945 | SCR_001797 | 2026-09-12 12:55:31 | 1 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
