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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Transcriptive Resource Report Resource Website |
Transcriptive (RRID:SCR_017545) | software application, data processing software, software resource, software toolkit, data analysis software | Software tool as bioinformatics analysis pipeline used for RNA sequencing data. Workflow processes raw data from FastQ inputs, aligns reads, generates gene and transcript counts, and performs quality control on results. | Analysis, pipeline, RNA, sequencing, data, raw, FastQ, input, align, read, gene, transcript, count, quality, control | Free, Available for download, Freely available | SCR_017545 | 2026-02-15 09:22:03 | 0 | |||||||||||
|
Vesselucida Explorer Resource Report Resource Website 1+ mentions |
Vesselucida Explorer (RRID:SCR_017674) | software application, data processing software, data analysis software, software resource | Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more. | MBF Bioscience, analysis, vasculature, specific, metric, segment, node, count, frequency, anastomoses, vessel, surface, volume | works with: Vesselucida 360 | Restricted | SCR_017674 | 2026-02-15 09:22:05 | 2 | ||||||||||
|
fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | software application, data processing software, data analysis software, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-02-15 09:22:11 | 23 | |||||||
|
SAVES Resource Report Resource Website 100+ mentions |
SAVES (RRID:SCR_018219) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server. | Structure validation, homology modeling, obtained model, analysis, validation server | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018219 | SAVES v5.0, Structure Analysis and Verification Server | 2026-02-15 09:21:34 | 183 | |||||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-02-15 09:22:11 | 2 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software application, data processing software, data analysis software, software resource | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick https://bio.tools/SpydrPick |
SCR_018176 | 2026-02-15 09:22:19 | 2 | ||||||
|
SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | software application, data processing software, data analysis software, software resource | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; Wellcome Trust ; Royal Society ; European Research Council |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-02-15 09:21:33 | 1 | ||||||||
|
MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | software application, data processing software, data analysis software, software resource | Software package for motion capture analysis by Innovision Systems Inc. | Motion capture, analysis, data, data tracking, Innovision Systems Inc. | Restricted | SCR_018188 | Innovision Systems MaxTRAQ software | 2026-02-15 09:21:33 | 1 | ||||||||||
|
NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | portal, data analysis service, service resource, production service resource, data or information resource, topical portal, analysis service resource | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | Neuroscience Multi-Omic Analytics | 2026-02-15 09:22:11 | 13 | ||||||||
|
ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | software application, data processing software, data analysis software, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-02-15 09:21:32 | 47 | ||||||
|
gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | software application, data processing software, data analysis software, software resource | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | gprofiler2 | 2026-02-15 09:22:19 | 53 | |||||||
|
QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | software application, data processing software, software resource, software toolkit, data analysis software | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | Quantify unknown Biophysics | 2026-02-15 09:22:18 | 2 | |||||||||
|
MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | software application, data processing software, software resource, software toolkit, data analysis software | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-02-15 09:22:10 | 6 | |||||||||||
|
UltraScan Resource Report Resource Website 10+ mentions |
UltraScan (RRID:SCR_018126) | software application, data processing software, data analysis software, software resource | Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis. | Hydrodynamic data, analytical ultracentrifugation experiment, data editing, analysis, sedimentation velocity experiment, spectrum analysis, genetic algorithm, Monte Carlo analysis | NSF DBI 9724273; NSF DBI 9974819; NSF ANI 228927; NSF TG-MCB 060019T; NSF TG-MCB 070038; NSF TG-MCB 070039; NSF TG-MCB 070040; NSF OCI 1032742; NSF ACI 1339649; NCRR RR022200; NCRR RR 022200 03S1; NIGMS GM120600; San Antonio Life Science Institute ; Howard Hughes Medical Institute ; Robert J. Kleberg Jr. and Helen C. Kleberg Foundation |
Free, Available for download, Freely available | SCR_018126 | 2026-02-15 09:21:32 | 20 | ||||||||||
|
Gene Expression Profiling Interactive Analysis Resource Report Resource Website 5000+ mentions |
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) | GEPIA | software resource, web service, data access protocol, service resource, production service resource, analysis service resource | Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis. | Cancer gene expression, normal gene expression, analysis, RNA sequencing, expression data, TCGA project, GTEx project, patient survival analysis, correlation analysis |
is related to: Gene Expression Profiling Interactive Analysis 2 has parent organization: Peking University; Beijing; China |
Cancer | Peking University ; National Natural Science Foundation of China |
PMID:28407145 | Free, Freely available | SCR_018294 | 2026-02-15 09:22:20 | 5635 | ||||||
|
Genie 2000 Basic Resource Report Resource Website 1+ mentions |
Genie 2000 Basic (RRID:SCR_021933) | software application, data processing software, software resource, data acquisition software, data analysis software | Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data. | Data acquisition, display, analysis, gamma and alpha spectrometry data | Restricted | SCR_021933 | Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic Spectroscopy Software, Marion Technologies Genie 2000 Basic | 2026-02-15 09:22:44 | 2 | ||||||||||
|
ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | data analysis service, service resource, production service resource, analysis service resource, resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-02-15 09:18:07 | 144 | ||||
|
TORTOISE Resource Report Resource Website 100+ mentions |
TORTOISE (RRID:SCR_001645) | TORTOISE | software application, image processing software, data processing software, software resource, image analysis software | An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data. | diffusion mri, dti, image motion correction, distortion correction, tensor computation, visualization, analysis, tensor fitting, modeling, magnetic resonance, tensor metric |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Diffusion MRI of Traumatic Brain Injury has parent organization: National Institute of Child Health and Human Development |
NICHD | Free, Available for download, Freely available | nlx_153921 | http://www.nitrc.org/projects/tortoise | SCR_001645 | Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble | 2026-02-15 09:18:08 | 101 | |||||
|
Gene Expression Omnibus (GEO) Resource Report Resource Website 10000+ mentions |
Gene Expression Omnibus (GEO) (RRID:SCR_005012) | GEO | database, service resource, storage service resource, data repository, data or information resource | Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries. | gold standard, genomics, data, repository, microarray, mRNA, DNA, protein, analysis, SAGE, mass spectrometry, dataset |
is used by: ChIPseeker is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is related to: Allen Institute for Brain Science has parent organization: NCBI works with: shinyGEO works with: Drug Gene Budger works with: Signaling Pathways Project works with: GEN3VA |
National Library of Medicine | PMID:23193258 PMID:21097893 PMID:18940857 PMID:17160034 PMID:17099226 PMID:16939800 PMID:16888359 PMID:15608262 PMID:11752295 |
r3d100010283, nif-0000-00142, nlx_96903, OMICS_01030, SCR_007303 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds http://www.ncbi.nlm.nih.gov/geo/ https://doi.org/10.17616/R33P44 |
http://www.ncbi.nlm.nih.gov/gds | SCR_005012 | Gene Expression Omnibus (GEO), Entrez GEO DataSets, Gene Expression Data Sets, Gene Expression Omnibus, GEO, NCBI GEO DataSets, GEO DataSets, Gene Expression Omnibus DataSets | 2026-02-15 09:18:52 | 11944 | ||||
|
Gene Weaver Resource Report Resource Website 10+ mentions |
Gene Weaver (RRID:SCR_003009) | data analysis service, database, service resource, storage service resource, data repository, production service resource, data or information resource, analysis service resource | Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. | phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Jackson Laboratory |
Integrative Neuroscience Initiative on Alcoholism ; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA R01 AA18776 |
PMID:22080549 PMID:19733230 |
Free, Freely available | r3d100012464, OMICS_02232, nif-0000-00517 | http://ontologicaldiscovery.org/ https://doi.org/10.17616/R3248T |
SCR_003009 | GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org | 2026-02-15 09:18:25 | 34 |
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.
