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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ReadCleaner4Scaffolding Resource Report Resource Website 1+ mentions |
ReadCleaner4Scaffolding (RRID:SCR_016166) | software application, software resource | This pipeline and the included scripts are used to filter useful reads for SSPACE. | SCR_016166 | 2026-08-09 09:06:59 | 1 | |||||||||||||
|
MVGC Multivariate Granger Causality Matlab Toolbox Resource Report Resource Website 10+ mentions |
MVGC Multivariate Granger Causality Matlab Toolbox (RRID:SCR_015755) | MVGC | software toolkit, software resource | Matlab software toolkit designed to facilitate Granger-causal analysis with multivariate and possibly multi-trial time series data. Annotated demonstration scripts are available which may be used as templates to assist in this the toolbox's functions. | granger causality, statistical inference, statistical analysis, time-series, multivariate, multi-trial, Matlab |
is used by: MATLAB has parent organization: University of Sussex; Brighton; United Kingdom |
EPSRC G/700543/1 | PMID:24200508 | GNU General Public License | SCR_015755 | MVGC Matlab® Toolbox, MVGC Matlab Toolbox | 2026-08-09 09:06:29 | 11 | ||||||
|
ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software toolkit, software resource | Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . | compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic | has parent organization: University of Pennsylvania; Philadelphia; USA | NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NEI EY022300; NHLBI HL134015; NLM LM009012; NLM LM010098; NLM LM011360; NCATS TR001263; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | Relief Based Algorithm Training Environment | 2026-08-09 09:07:11 | 0 | ||||||
|
Bionitio Resource Report Resource Website 1+ mentions |
Bionitio (RRID:SCR_017259) | software toolkit, software resource | Open source software tool to provide template for command line bioinformatics tools in various programming languages. Program reads one or more input FASTA files, computes variety of statistics on each file, and prints tabulated output. Used as basis for learning and as foundation for starting new projects. | template, command, line, bioinformatic, tool, programming, language, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Melbourne; Victoria; Australia |
Free, Available for download, Freely available | biotools:bionitio | https://bio.tools/Bionitio | SCR_017259 | 2026-08-09 09:07:01 | 2 | ||||||||
|
MuseScore Resource Report Resource Website 10+ mentions |
MuseScore (RRID:SCR_016161) | software application, software resource | Music composition and manipulation software. | SCR_016161 | 2026-08-09 09:06:37 | 34 | |||||||||||||
|
Fastahack Resource Report Resource Website 1+ mentions |
Fastahack (RRID:SCR_016090) | software application, software resource | Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths. | extract, quickly, subsequence, sequence, FASTA, files, generate, index |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_20516 | https://packages.debian.org/stretch/fastahack, https://sources.debian.org/src/fastahack/ | SCR_016090 | 2026-08-09 09:06:35 | 1 | ||||||||
|
Fastaq Resource Report Resource Website 10+ mentions |
Fastaq (RRID:SCR_016091) | software toolkit, software resource | Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together. | diverse, script, collect, filter, merge, split, sort, trim, search, replace, file, single-letter code, nucleotide, sequence, peptide, amino acid, text-based, format |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | OMICS_19987 | https://sources.debian.org/src/fastaq/ | SCR_016091 | 2026-08-09 09:06:51 | 25 | ||||||||
|
Autopatcher Resource Report Resource Website 1+ mentions |
Autopatcher (RRID:SCR_017464) | software application, software resource | Software tool for neuronal recording in intact brain. | Neuronal, recording, intact, brain, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH106027 | PMID:29297466 | Free, Available for download, Freely available | SCR_017464 | 2026-08-09 09:07:17 | 2 | ||||||||
|
Fastqtl Resource Report Resource Website 100+ mentions |
Fastqtl (RRID:SCR_016093) | Fastqtl | software toolkit, software resource | Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq. | molecular, phenotype, multiply, testing, genotype, correct, genomic dataset, trait, loci, cis, quantitative, multi dimensional |
is listed by: Debian is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
European Commission SYSCOL FP7; European Research Council ; Louis Jeantet Foundation ; Swiss National Science Foundation ; SystemsX ; NIH-NIMH (GTEx) ; Helse Sør Øst |
PMID:26708335 | Free, Available for download | OMICS_10934 | https://sources.debian.org/src/fastqtl/ | SCR_016093 | Fastqtl: Fast quantitative trait loci | 2026-08-09 09:06:35 | 133 | ||||
|
Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software toolkit, software resource | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools, https://sources.debian.org/src/harvest-tools/ | SCR_016132 | 2026-08-09 09:06:36 | 4 | ||||||
|
R package: RVAideMemoire Resource Report Resource Website 100+ mentions |
R package: RVAideMemoire (RRID:SCR_015657) | software toolkit, software resource | Software package that contains miscellaneous functions useful in biostatistics, such as univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions shorten existing procedures and implement plotting functions that can be used with a variety of methods and packages. | statistical analysis, biostatistics, multivariate testing, permutation, plotting function, graphical function | is listed by: CRAN | Free, Available for download | SCR_015657 | RVAideMemoire, RVAideMemoire: Testing and Plotting Procedures for Biostatistics, Package 'RVAideMemoire' | 2026-08-09 09:06:54 | 157 | |||||||||
|
Stim2 Resource Report Resource Website 1+ mentions |
Stim2 (RRID:SCR_016751) | software application, software resource | Software environment for custom stimulus and task design as well as presentation. Compumedics Neuroscan’s design system which can be integrated in fMRI, MEG, and other functional neuro-imaging applications. Provides interface to design and present visual and auditory stimulation paradigms. | Compumedics Neuroscan, stimulus, task, design, presentation, fMRI, MEG, neuroimaging, visual, auditory | Commercially available | SCR_016751 | 2026-08-09 09:07:06 | 3 | |||||||||||
|
Lenntech activity coefficient calculator Resource Report Resource Website 1+ mentions |
Lenntech activity coefficient calculator (RRID:SCR_016475) | software application, software resource | Software tool to calculate the activity coefficient of an ion in solution by Lenntech B.V. Determines the ionic strength of solution by using the concentration of ions present in drinking water. | program, calculate, activity, coefficient, ion, solution, strength, concentration, drinking, water, Lenntech | Free, Public | SCR_016475 | 2026-08-09 09:06:59 | 2 | |||||||||||
|
Chromeleon Chromatography Data System (CDS) Software Resource Report Resource Website 10+ mentions |
Chromeleon Chromatography Data System (CDS) Software (RRID:SCR_016874) | CDS | software toolkit, software resource | Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results. | Thermofisher, system, chromatography, operation, data, quality, manage, analytical, process, instrument, control | Commercially available | SCR_016874 | Chromeleon Chromatography Data System, Chromeleon Chromatography Data System (CDS), Dionex Chromeleon7 | 2026-08-09 09:07:07 | 11 | |||||||||
|
spm_auto_reorient_coregister Resource Report Resource Website |
spm_auto_reorient_coregister (RRID:SCR_017281) | software toolkit, software resource | Open source cross platform for automatic AC-PC realignment, reorientation and coregistration robust to brain damage in Statistical Parametric Mapping. Set of routines to perform auto reorient and auto coregistration in toolbox SPM12. | Nifti Libraries, NeuroImaging, MRI, MRI 3D image, reorientation, coregistration, statistical, parametric, mapping | works with: SPM | FNRS 1124417F | Free, Available for download, Freely available | SCR_017281 | 2026-08-09 09:07:02 | 0 | |||||||||
|
DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software toolkit, software resource | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-08-09 09:07:07 | 2 | ||||||||
|
Scope Resource Report Resource Website 10+ mentions |
Scope (RRID:SCR_017454) | software application, software resource | Two photon microscope control software with multi area capabilities. | Two, photon, microscope, control, BRAIN Initiative | is recommended by: BRAIN Initiative | NINDS NS090475 | Free, Available for download, Freely available | SCR_017454 | 2026-08-09 09:07:20 | 15 | |||||||||
|
pyRayleighCuda Resource Report Resource Website |
pyRayleighCuda (RRID:SCR_017453) | software application, software resource | Python Rayleigh-Sommerfeld integral for acoustics with optional CUDA graphics processing unit (GPU) implementation. | Rayleigh-Sommerfeld, integral, acoustics, CUDA, graphics, processing, unit, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH109105 | Free, Freely available | SCR_017453 | 2026-08-09 09:07:04 | 0 | |||||||||
|
PyNWB Resource Report Resource Website 1+ mentions |
PyNWB (RRID:SCR_017452) | software application, software resource | Software Python package for working with Neurodata stored in Neurodata Without Borders files. Software providing API allowing users to read and create NWB formatted HDF5 files. Developed in support to NWB project with aim of spreading standardized data format for cellular based neurophysiology information. | Neurodata, stored, NWB, file, share, standardized, data, format, neurophysiology, BRAIN Initiative |
uses: Hierarchical Data Modeling Framework is used by: NWB Explorer is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Neurodata Without Borders is related to: Neurodata Extensions Catalog is related to: HDMF Common Schema is related to: NWB Inspector |
Kavli Foundation ; General Electric ; Howard Hughes Medical Institute ; Allen Institute for Brain Science ; NSF 0855272; International Neuroinformatics Coordinating Facility ; NIH BRAIN Initiative R24 MH116922 |
PMID:26590340 | Free, Available for downloading, Freely available | https://github.com/NeurodataWithoutBorders/pynwb | https://github.com/AllenInstitute/nwb-api | SCR_017452 | 2026-08-09 09:07:16 | 4 | ||||||
|
viridis Resource Report Resource Website 10+ mentions |
viridis (RRID:SCR_016696) | software toolkit, software resource | Software package which brings to R color scales. Created for the Python matplotlib library. | R, color, scale, Python, matplotlib, CRAN |
is affiliated with: R Project for Statistical Computing is affiliated with: CRAN |
Free, Available for download, Freely available | https://github.com/sjmgarnier/viridis | SCR_016696 | 2026-08-09 09:06:48 | 30 |
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.
