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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Network Analysis, Visualization and Graphing TORonto Resource Report Resource Website 50+ mentions |
Network Analysis, Visualization and Graphing TORonto (RRID:SCR_008373) | NAViGaTOR | software application, data processing software, d visualization software, software resource, data visualization software | A software package for visualizing and analyzing protein-protein interaction networks. NAViGaTOR can query OPHID / I2D - online databases of interaction data - and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms. NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as GO and the Proteomics Standards Initiative (PSI). NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems. NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches. | fly, algorithm, capacity, graphical, graphing, human, interaction, interactome, intersection, mouse, network, node, protein, proteomic, rat, worm, yeast, graphing application, 2d visualization, 3d visualization, visualization, biological network, protein-protein interaction, gene, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Genomics Institute ; Canada Research Chair Program ; Ontario Research Fund Research Excellence ; Canada Foundation for Innovation 12301; Canada Foundation for Innovation 203383 |
PMID:19837718 | Freely-downloadable for academic and not-for-profit institutions | nif-0000-25610, biotools:navigator | https://bio.tools/navigator | SCR_008373 | NAViGaTOR - Network Analysis Visualization and Graphing TORonto, NAViGaTOR - Network Analysis Visualization & Graphing TORonto | 2026-02-17 10:01:21 | 52 | ||||
|
Eukaryote Genes Resource Report Resource Website 10+ mentions |
Eukaryote Genes (RRID:SCR_008617) | data or information resource, database | Provides summary of gene and genomic information from eukaryotic organism databases. This includes gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, product information, links to extended gene information. | eukaryote, eukaryotic gene ontology, eukaryotic genome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Indiana University Center for Genomics and Bioinformatics ; NSF DBI 0090782; NSF DBI 9982851 |
Free, Freely available | nif-0000-31969, biotools:eugenes, SCR_013197, nif-0000-02818 | https://bio.tools/eugenes | SCR_008617 | euGenes | 2026-02-17 10:01:08 | 17 | ||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | data access protocol, production service resource, analysis service resource, source code, service resource, software resource, web service, data analysis service | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/ https://bio.tools/sift https://sources.debian.org/src/sift/ |
http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-02-17 10:02:18 | 10223 | |||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, software application, data processing software, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs https://sources.debian.org/src/macs/ |
SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-02-17 10:02:23 | 1325 | ||||
|
GeneProf Resource Report Resource Website 10+ mentions |
GeneProf (RRID:SCR_012927) | GeneProf | data access protocol, data or information resource, production service resource, analysis service resource, database, service resource, software resource, web service, data analysis service | A database of curated, integrated and reusable high-throughput genomics experiments and a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; Next-Generation Sequencing or NGS). Algorithm developers and computer programmers can develop their own modules and extend the functionality of GeneProf. Existing software can be easily wrapped and integrated in the GeneProf framework and data from GeneProf may be used externally. | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Edinburgh; Scotland; United Kingdom |
MRC ; European Union Framework 7 Project EuroSyStem |
PMID:22205509 PMID:24174536 |
Acknowledgement requested | biotools:geneprof, OMICS_00442 | https://bio.tools/geneprof | SCR_012927 | 2026-02-17 10:02:20 | 15 | |||||
|
PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | software application, data processing software, data analysis software, software resource, simulation software | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-02-17 10:02:22 | 4151 | |||||
|
IUPHAR/BPS Guide to Pharmacology Resource Report Resource Website 1000+ mentions |
IUPHAR/BPS Guide to Pharmacology (RRID:SCR_013077) | IUPHAR Database, IUPHAR-DB, IUPHAR GPCR, IUPHAR RECEPTOR | narrative resource, data or information resource, database, standard specification, portal | Portal and searchable database of pharmacological information. Information is presented at two levels, the initial view or landing pages for each target family provide expert-curated overviews of the key properties and the available selective ligands and tool compounds. For selected targets, more detailed introductory chapters for each family are available along with curated information on the pharmacological, physiological, structural, genetic and pathophysiogical properties of each target. | pharmacology, drug discovery, portal, guide, physiology, molecular structure, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: NC-IUPHAR |
Wellcome Trust | PMID:21087994 | nif-0000-03056, biotools:iuphar-db, r3d100013308 | https://bio.tools/iuphar-db https://doi.org/10.17616/R31NJMRG |
http://www.iuphar-db.org | SCR_013077 | International Union of Pharmacology Database, International Union of Basic and Clinical Pharmacology Database | 2026-02-17 10:02:21 | 2259 | ||||
|
Pathway Tools Resource Report Resource Website 10+ mentions |
Pathway Tools (RRID:SCR_013786) | data management software, software application, software resource, software toolkit | A software application which supplies software tools to develop and maintain pathway/genome databases (PGDBs). These include the development of organism-specific databases, metabolic reconstruction and metabolic-flux modeling, scientific visualization and web publishing of organism-specific databases, analysis of gene-expression and metabolomics datasets, comparative genome and pathway analyses, and analysis of biological networks. | software application, bioinformatics, software, software system, pathway genome database, PGDB, bio.tools |
is used by: BioCyc is used by: EcoCyc is used by: MetaCyc is listed by: BioCyc is listed by: bio.tools is listed by: Debian is related to: BioCyc is related to: MetaCyc is related to: EcoCyc is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: BioCyc |
NIGMS GM077678; NIGMS GM080746; NIGMS GM75742 |
DOI:10.1093/bib/bbp043 | biotools:pathway_tools | http://bioinformatics.ai.sri.com/ptools/ptools-overview.html https://bio.tools/pathway_tools |
SCR_013786 | Pathway Tools Bioinformatics Software, Pathway Tools Software | 2026-02-17 10:02:37 | 23 | ||||||
|
Metabolomics Workbench Resource Report Resource Website 500+ mentions |
Metabolomics Workbench (RRID:SCR_013794) | MetWB | data or information resource, service resource, data repository, storage service resource | Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops. | repository, metabolomics, database, funding, training, protocol, bio.tools, FASEB list |
is used by: NIH Heal Project 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 lists: NIH Metabolomics program lists: MetaCore lists: JMP lists: STATISTICA lists: Spotfire lists: Coordination of Standards in Metabolomics lists: MetaboLights lists: MetabolomeXchange lists: Metabolomics Society lists: Birmingham Metabolite Library lists: Glycan Mass Spectral Database (GMDB) lists: Mass Spectral Library lists: mzCloud lists: MetabolomeExpress lists: Spectral Database System (SDBS) lists: CTSgetR lists: Hierarchical Clustering lists: imDEV lists: Linear Discriminant Analysis lists: Principal Components Analysis lists: mwtabR lists: 3Omics lists: ACD/ NMR Processor lists: NIST Mass Spectrometry Data Center lists: Chemical Translation Service lists: Chenomx NMR Suite lists: DeviumWeb lists: MBRole lists: MetaMapR lists: MetaP lists: Metscape lists: SIMCA lists: TeachingDemos is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is listed by: re3data.org is listed by: DataCite has parent organization: University of California; California; USA is parent organization of: Metabolomics Workbench Metabolite Database |
NIH | Free, Freely available | biotools:Metabolomics_Workbench | https://bio.tools/Metabolomics_Workbench https://api.datacite.org/dois?prefix=10.21228 |
SCR_013794 | , Metabolomics Workbench, MetWB, UCSD Metabolomics Workbench, Metabolomics Workbench (MetWB) | 2026-02-17 10:02:03 | 534 | |||||
|
OsiriX Medical Imaging Software Resource Report Resource Website 1000+ mentions |
OsiriX Medical Imaging Software (RRID:SCR_013618) | data visualization software, data processing software, software application, software resource | :OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. : | bio.tools |
is listed by: bio.tools is listed by: Debian |
biotools:osirix, nif-0000-00340 | https://bio.tools/osirix | SCR_013618 | OsiriX | 2026-02-17 10:02:24 | 1374 | ||||||||
|
Membrane Protein Explorer Resource Report Resource Website 10+ mentions |
Membrane Protein Explorer (RRID:SCR_014077) | MPEx | data analysis software, software application, data processing software, software resource | Software which predicts topology and other features of membrane proteins through hydropathy plots based on thermodynamic and biological principles. This version of MPEx uses two types of hydropathy scales: Experiment-based whole-residue partitioning scales and experiment-based biological partitioning scales. The whole-residue partitioning scales predict the transmembrane (TM) segments of membrane proteins of known structure. The biological scale utilizes current knowledge of the code the Sec61 translocon to identify TM segments. MPEx is a Java program (not a Java applet) deployed using Java Web Start, which is part of the Java Runtime Environment. | membrane protein, hydropathy plot, topology, software, java, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Irvine; California; USA |
PMID:19785006 | Available to the research community, Requires version 7 or higher of Java Runtime Environment | biotools:mpex | https://bio.tools/mpex | SCR_014077 | Membrane Protein Explorer (MPEx) | 2026-02-17 10:02:32 | 34 | |||||
|
Buccaneer Resource Report Resource Website 100+ mentions |
Buccaneer (RRID:SCR_014221) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software which performs statistical chain tracing by identifying connected alpha-carbon positions using a likelihood-based density target. The target distributions are generated by a simulation calculation using a known reference structure for which calculated phases are available. The success of the method is dependent on the features of the reference structure matching those of the unsolved work structure. For almost all cases, a single reference structure can be used, with modifications automatically applied to the reference structure to match its features to the work structure. | statistical chain tracing, alpha carbon position, sequence analysis software, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:16929101 | biotools:buccaneer | https://bio.tools/buccaneer | SCR_014221 | buccaneer - Statistical protein chain tracing | 2026-02-17 10:02:35 | 332 | |||||||
|
FluoRender Resource Report Resource Website 100+ mentions |
FluoRender (RRID:SCR_014303) | software application, data processing software, data analysis software, software resource, data visualization software | Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation. | rendering tool, confocal microscopy data visualization, neurobiology, fluorescent stain, brain, bio.tools |
is used by: VVD Viewer is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
Free, Available for download, Freely available | biotools:fluorender | https://bio.tools/fluorender | SCR_014303 | FluoRender Visualization | 2026-02-17 10:02:09 | 127 | |||||||
|
NiftyFit Resource Report Resource Website 1+ mentions |
NiftyFit (RRID:SCR_014301) | software library, software resource, software toolkit | Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T | software library, voxel wise fit, relaxometry, mri, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
MRC ; NIHR ; EPSRC ; NIHR BRC |
PMID:26972806 | Free, Available for download, Freely available | biotools:niftyfit, BioTools:niftyfit | https://github.com/KCL-BMEIS/niftyreg https://bio.tools/niftyfit https://bio.tools/niftyfit https://bio.tools/niftyfit |
SCR_014301 | 2026-02-17 10:02:36 | 9 | ||||||
|
SortMeRNA Resource Report Resource Website 500+ mentions |
SortMeRNA (RRID:SCR_014402) | software application, data processing software, data analysis software, software resource, sequence analysis software | Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis software, filter, map, otu picking, ngs, sort, rna, rrna, bio.tools |
uses: QIIME is listed by: Debian is listed by: bio.tools |
PMID:23071270 DOI:10.1093/bioinformatics/bts611 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02619, biotools:sortmerna | https://bio.tools/sortmerna https://sources.debian.org/src/sortmerna/ |
SCR_014402 | 2026-02-17 10:02:11 | 621 | |||||||
|
Mascot Resource Report Resource Website 5000+ mentions |
Mascot (RRID:SCR_014322) | software application, standalone software, data processing software, software resource, signal processing software | A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters. | server, software package, mass spectrometry, protein, identify, characterize, bio.tools |
is used by: MSQuant is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: MascotScan |
Free, Can be licensed for in-house use, Available for download | biotools:MASCOT | http://www.matrixscience.com/search_intro.html https://bio.tools/MASCOT |
SCR_014322 | Mascot Server | 2026-02-17 10:02:37 | 6896 | |||||||
|
OpenWorm Resource Report Resource Website 10+ mentions |
OpenWorm (RRID:SCR_014650) | software application, web application, software resource, simulation software | 3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders. | simulation, model, web application, web browser, c elegans, nematode, worm, roundworm, open source, 3d, dissect, anatomy, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: WormBase is hosted by: GitHub |
PMID:25404913 DOI:10.3389/fncom.2014.00137 |
Open source, Code is available on GitHub, Available on the App Store | SCR_014984, biotools:OpenWorm | https://bio.tools/OpenWorm | SCR_014650 | OpenWorm Browser, Open Worm | 2026-02-17 10:02:15 | 21 | ||||||
|
ProtTest Resource Report Resource Website 1000+ mentions |
ProtTest (RRID:SCR_014628) | software application, web application, data processing software, data analysis software, software resource | Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bioinformatics, model, best fit model, protein evolution, amino acid replacement, server, bio.tools |
uses: PhyML is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is hosted by: GitHub |
PMID:15647292 DOI:10.1093/bioinformatics/btr088 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11547, biotools:prottest | https://github.com/ddarriba/prottest3 https://bio.tools/prottest https://sources.debian.org/src/prottest/ |
SCR_014628 | 2026-02-17 10:02:43 | 1981 | |||||||
|
CummeRbund Resource Report Resource Website 100+ mentions |
CummeRbund (RRID:SCR_014568) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions. | r software, cufflink, rna-seq, sqlite, gene, transcript, transcription start site, cds region, r, rnaseq, rna seq, bio.tools, FASEB list |
uses: R Project for Statistical Computing is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; has parent organization: Harvard University; Cambridge; United States |
Free, Freely available | biotools:cummerbund, OMICS_07349 | https://bio.tools/cummerbund https://sources.debian.org/src/r-bioc-cummerbund/ |
SCR_014568 | 2026-02-17 10:02:42 | 361 | ||||||||
|
ggplot2 Resource Report Resource Website 10000+ mentions |
ggplot2 (RRID:SCR_014601) | data visualization software, data processing software, software application, software resource | Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers. | plotting system, r, graphics, data analysis, multi-layered graphics, bio.tools |
uses: ggpubr uses: ggeffects uses: ggsignif is used by: riboWaltz is used by: ClustVis is used by: ggrepel is used by: PlotsOfData is used by: EnhancedVolcano is used by: tidyverse is used by: ComplexUpset is used by: ggfortify is used by: forestmodel is used by: ggvenn is used by: metaviz is used by: ggVennDiagram is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: ggraph is related to: ggbiplot is related to: GGally has parent organization: CRAN works with: Plotly works with: cowplot works with: ggalluvial works with: ggforce works with: ggbreak works with: ggrastr works with: tidybayes works with: ggsurvfit works with: ggtext works with: ggsci |
Free, Freely available | biotools:ggplot2 | http://docs.ggplot2.org/current/ https://github.com/tidyverse/ggplot2 https://bio.tools/ggplot2 |
http://ggplot2.org/ | SCR_014601 | grammar of graphics plot2 | 2026-02-17 10:02:14 | 36105 |
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