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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
UCSF Chimera Resource Report Resource Website 1000+ mentions |
UCSF Chimera (RRID:SCR_004097) | Chimera | software application, d visualization software, data processing software, software resource | Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. | molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures |
is used by: Structure-function linkage database is listed by: 3DVC is listed by: SoftCite is related to: Integrative Modeling Platform is related to: UCSF ChimeraX is related to: UCSF ChimeraX has parent organization: Resource for Biocomputing Visualization and Informatics |
NIGMS P41 GM103311; NCRR P41 RR001081 |
PMID:15264254 | Restricted | nlx_143560 | http://plato.cgl.ucsf.edu/chimera/ | SCR_004097 | Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System | 2026-02-15 09:18:40 | 2078 | ||||
|
FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | software application, sequence analysis software, data processing software, software resource, data analysis software | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/ https://bio.tools/flash https://sources.debian.org/src/flash/ |
SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-02-15 09:18:58 | 2175 | ||||
|
RAxML Resource Report Resource Website 10000+ mentions |
RAxML (RRID:SCR_006086) | RAxML | software application, data processing software, data analysis software, software resource | Software program for phylogenetic analyses of large datasets under maximum likelihood. | phylogeny, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: RAxML Next Generation works with: PAML |
PMID:24451623 PMID:16928733 PMID:15608047 DOI:10.1093/bioinformatics/btu033 |
GNU General Public License | biotools:raxml, OMICS_02242 | https://bio.tools/raxml https://sources.debian.org/src/raxml/ |
SCR_006086 | Randomized Axelerated Maximum Likelihood | 2026-02-15 09:19:08 | 12473 | |||||
|
GraphPad Prism Resource Report Resource Website 10000+ mentions Rating or validation data |
GraphPad Prism (RRID:SCR_002798) | software application, data visualization software, data processing software, software resource, data analysis software | Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling. | biostatistics, curve, fitting, nonlinear, regression, graphing, statistical, analysis, biology, pharmacology, physiology |
is listed by: SoftCite has parent organization: GraphPad |
Restricted | rid_000081, SCR_015807 | https://www.graphpad.com/updates/prism-920-release-notes http://graphpad-prism.software.informer.com/5.0/ https://www.graphpad.com/guides/prism/7/user-guide/index.htm |
SCR_002798 | Prism 9.2.0, Graph Pad Prism 7, Graph Pad Prism, GraphPad Prism, Graph pad Prism 5, GraphPad Prism version 9.2.0, Graphpad Prism software, Graph pad Prism 8, Graph pad Prism, Graphpad Prism | 2026-02-15 09:18:23 | 46700 | |||||||
|
Clustal W2 Resource Report Resource Website 5000+ mentions |
Clustal W2 (RRID:SCR_002909) | software application, data processing software, software resource, alignment software, service resource, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF. | multiple, sequence, alignment, cladogram, phylogram, evolution, phylogenetic, tree, protein, nucleic, acid, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Clustal Omega is related to: UniProt is related to: Clustal Omega is related to: VectorBase is related to: TopoSNP is related to: Clustal 2 has parent organization: European Bioinformatics Institute has parent organization: University College Dublin; Dublin; Ireland |
Science Foundation Ireland | PMID:17846036 PMID:20439314 DOI:10.1093/bioinformatics/btm404 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02562, nif-0000-30076 | http://www.ch.embnet.org/software/ClustalW.html https://sources.debian.org/src/clustalx/ |
http://www.ebi.ac.uk/tools/clustalw/ | SCR_002909 | European Bioinformatics Institute - ClustalW2 | 2026-02-15 09:18:26 | 7830 | ||||
|
SPSS Resource Report Resource Website 10000+ mentions |
SPSS (RRID:SCR_002865) | SPSS | software application, data analytics software, software toolkit, software resource | Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. | IBM, data, collection, statistics, predict, analyze |
is listed by: SoftCite is related to: IBM SPSS Statistics |
Restricted | SCR_017473, rid_000042 | https://www.ibm.com/products/software | SCR_002865 | Statistical Package for the Social Sciences, IBM SPSS Statistics:International Business Machines SPSS Statistics, IBM SPSS v18, IBM SPSS v17, IBM SPSS v16 | 2026-02-15 09:18:24 | 108532 | ||||||
|
Haploview Resource Report Resource Website 5000+ mentions |
Haploview (RRID:SCR_003076) | Haploview | software application, source code, data processing software, software resource | A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site. | linkage disequilibrium, haplotype, genotype, visualization, analysis, single nucleotide polymorphism, gene, genetic, genomic, java |
is listed by: Genetic Analysis Software is listed by: SoftCite is related to: International HapMap Project is related to: PLINK has parent organization: Broad Institute |
PMID:15297300 PMID:21356869 PMID:20147036 |
Free, Available for download, Freely available | nif-0000-30472 | http://www.broad.mit.edu/personal/jcbarret/haploview/ | SCR_003076 | 2026-02-15 09:18:26 | 6933 | ||||||
|
NIH Image Resource Report Resource Website 1000+ mentions |
NIH Image (RRID:SCR_003073) | NIH Image | software application, image processing software, data processing software, software resource, source code, image analysis software | Public image processing and analysis program for Macintosh. | image processing application, public image processing software, imagej |
is listed by: SoftCite is related to: ImageJ is related to: BrainImage Software is related to: Object-Image has parent organization: National Institutes of Health has parent organization: National Institute of Mental Health |
NINDS ; NIMH |
Free, download Freely available | nif-0000-30469 | https://imagej.net/nih-image/index.html | SCR_003073 | 2026-02-15 09:18:28 | 4412 | ||||||
|
Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | software application, data visualization software, data processing software, software resource, data analysis software | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-02-15 09:18:26 | 23431 | |||||
|
BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | source code, software resource, wiki, data or information resource, narrative resource, software repository, software toolkit | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl https://sources.debian.org/src/bioperl/ |
SCR_002989 | 2026-02-15 09:18:25 | 402 | |||||
|
RNAhybrid Resource Report Resource Website 100+ mentions |
RNAhybrid (RRID:SCR_003252) | RNAhybrid | data analysis service, software resource, service resource, production service resource, analysis service resource | Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. | microrna, target prediction, free energy, rna, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15383676 DOI:10.1261/rna.5248604 |
Free, Available for download, Freely available | OMICS_00416, biotools:rnahybrid, nif-0000-31412 | https://bio.tools/rnahybrid https://sources.debian.org/src/rnahybrid/ |
SCR_003252 | 2026-02-15 09:18:28 | 477 | ||||||
|
GeneChip Operating Software Resource Report Resource Website 500+ mentions |
GeneChip Operating Software (RRID:SCR_003408) | GCOS | software application, sequence analysis software, data processing software, software resource, data analysis software | Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request. | gene expression, snp mapping, resequencing, analysis, genotyping, platform, software, comparison, analysis |
is listed by: Biositemaps is listed by: SoftCite has parent organization: Scripps Research Institute |
Free, Available for download, Freely available | nif-0000-33019 | https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/genechip-operating-software-service-pack-2-software-update.html | SCR_003408 | GeneChip Operating Software (GCOS), DNA Array Core Facility GeneChip Operating Software, DNA Array Core Facility GeneChip Operating Software (GCOS) | 2026-02-15 09:18:30 | 649 | ||||||
|
IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | software application, image processing software, data processing software, software resource, source code, image analysis software | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-02-15 09:18:32 | 1585 | ||||
|
PyMOL Resource Report Resource Website 1000+ mentions |
PyMOL (RRID:SCR_000305) | software application, data visualization software, data processing software, software resource, 3d visualization software | A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures. | visualization, molecule, 3d, molecular structure visualization, molecular visualization system, |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Restricted | nlx_156834, OMICS_03802 | https://sources.debian.org/src/pymol/ | SCR_000305 | 2026-02-15 09:17:54 | 3422 | ||||||||
|
Treerecs Resource Report Resource Website 1+ mentions |
Treerecs (RRID:SCR_024497) | software application, software resource | Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree. | species and gene tree reconciliation, integrated phylogenetic, from sequences to reconciliations, correct gene trees, rearrange gene trees, reroot gene trees, | is listed by: SoftCite | PMID:33085745 | Free, Available for download, Freely available | https://project.inria.fr/treerecs/ | SCR_024497 | 2026-02-15 09:23:45 | 1 | ||||||||
|
Evalue Resource Report Resource Website 10+ mentions |
Evalue (RRID:SCR_024506) | web application, source code, software resource | Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences. | E-value calculator, compute E-values for variety of outcome measures, | is listed by: SoftCite | PMID:29912013 | Free, Available for download, Freely available | https://github.com/mayamathur/evalue_package | SCR_024506 | 2026-02-15 09:22:43 | 14 | ||||||||
|
qBasePLUS Resource Report Resource Website 100+ mentions |
qBasePLUS (RRID:SCR_003370) | qbase+ | commercial organization, software resource | Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology. | real-time quantitative pcr |
is listed by: OMICtools is listed by: SoftCite is related to: geNORM has parent organization: Biogazelle |
PMID:17291332 | Free, Available for download, Freely available | OMICS_02320 | https://biogazelle-qbaseplus.software.informer.com/2.0/ | http://medgen.ugent.be/qbase/ | SCR_003370 | 2026-02-15 09:18:30 | 343 | |||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | source code, software toolkit, software resource | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/ https://github.com/broadinstitute/picard https://sources.debian.org/src/picard-tools/ |
SCR_006525 | 2026-02-15 09:19:17 | 14139 | ||||||||
|
Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | data management software, software application, data analytics software, software resource | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html https://www.sas.com/en_us/software/sas9.html |
SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.4 | 2026-02-15 09:19:52 | 7165 | ||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software application, software resource | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciPy, Scientific Tools for Python | 2026-02-15 09:19:27 | 12935 |
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.
