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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Marshall BioResources Resource Report Resource Website 10+ mentions |
Marshall BioResources (RRID:SCR_015489) | biomaterial supply resource, material resource, organism supplier | Commercial provider of purpose-bred animals for biomedical research. They provide dogs, pigs, ferrets, mice, and guinea pigs in physically and psychologically healthy condition. | animal provider, purpose bred animal, beagle, hound, mongrel, minipig, influenza free ferret | is recommended by: Assessment and Accreditation of Laboratory Animal Care International | SCR_015489 | 2026-08-08 12:00:24 | 34 | |||||||||||
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Atomify LAMMPS Resource Report Resource Website 1+ mentions |
Atomify LAMMPS (RRID:SCR_015240) | mobile app, software resource, software application, simulation software | Mobile simulation app for visualizing molecular interactions in liquids, solids and gases. The simulations are performed with the molecular dynamics code LAMMPS. | molecular physics, molecular simulation, molecular interaction | Open source, Available for Android phones | SCR_015240 | Atomify | 2026-08-08 12:00:39 | 6 | ||||||||||
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Encode Resource Report Resource Website 1000+ mentions |
Encode (RRID:SCR_015482) | data or information resource, data set, consortium, portal, organization portal | Consortium to build comprehensive parts list of functional elements in human genome. This includes elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Data from 2012-present. | genome, sequencing, protein, rna, dna, consortium |
is related to: modENCODE is related to: ENCODE is related to: 3D Genome has parent organization: Stanford University; Stanford; California has parent organization: University of California at Santa Cruz; California; USA |
NHGRI HG006992 | PMID:15499007 | Free, Freely available | SCR_015482 | ENCODE Project | 2026-08-08 12:00:24 | 1293 | |||||||
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Transcriptome architecture of adult mouse brain Resource Report Resource Website 1+ mentions |
Transcriptome architecture of adult mouse brain (RRID:SCR_015483) | data or information resource, image collection | Image collection of transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images. | mouse brain architecture, mouse brain image, in situ hybridization image | DOI:10.1007/s12021-017-9333-1 | Public | SCR_015483 | 2026-08-08 12:00:37 | 2 | ||||||||||
|
SEER Resource Report Resource Website 500+ mentions |
SEER (RRID:SCR_015499) | sequence analysis software, software resource, software application, source code, data analysis software, data processing software | Sequence element enrichment analysis tool to perform pan-genome-wide association studies in bacteria. | bacterial genome association, sequence element enrichment analysis, kmer enrichment analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1038/ncomms12797 DOI:10.1101/038463 |
Available for download | OMICS_21699 | https://sources.debian.org/src/seer/ | SCR_015499 | 2026-08-08 12:00:37 | 547 | |||||||
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MMPC-University of Michigan Medical School Resource Report Resource Website 1+ mentions |
MMPC-University of Michigan Medical School (RRID:SCR_015373) | data or information resource, access service resource, resource, topical portal, service resource, portal, disease-related portal | Research center which aims to contribute to a national database of metabolic phenotyping data in wild-type mouse strains and a broad range of mouse models relevant to the pathogenesis and treatment of diabetes, obesity and associated metabolic disorders. It also aims to foster continued technical development, refinement of assay sensitivity and specificity, data reproducibility, and transmission of best research practices within the areas of fundamental and applied diabetes and obesity research. | diabetes research center, obesity research center, mouse model research |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Mouse Metabolic Phenotyping Centers has parent organization: University of Michigan; Ann Arbor; USA is parent organization of: MMPC-University of Michigan Medical School Microbiome Core is parent organization of: MMPC-University of Michigan Medical School Microvascular Complications Core is parent organization of: MMPC-University of Michigan Medical School Metabolism Bariatric Surgery and Behavior Core is parent organization of: MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core has organization facet: MMPC-University of Michigan Medical School Microbiome Core has organization facet: MMPC-University of Michigan Medical School Animal Care and Germ-Free Mouse Core has organization facet: MMPC-University of Michigan Medical School Metabolism Bariatric Surgery and Behavior Core has organization facet: MMPC-University of Michigan Medical School Microvascular Complications Core is organization facet of: National Mouse Metabolic Phenotyping Centers |
NIDDK U2C-DK110768 | Available to the research community, Acknowledgement requested | SCR_015373 | 2026-08-08 12:00:36 | 1 | |||||||||
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Autodesk Meshmixer Resource Report Resource Website 100+ mentions |
Autodesk Meshmixer (RRID:SCR_015736) | authoring tool, 3d visualization software, software resource, software application, data visualization software, data processing software | 3D visualization software for working with triangle meshes. This software also can clean up 3D scans, design objects for 3D printing, and perform other 3D design-related functions. | 3d, 3d visualization, 3d printing, triangle mesh, 3d scan, 3d design | PMID:28663663 | Free, Available for download, Runs on Mac OS, Runs on Windows | http://www.mmmanual.com/ | SCR_015736 | MeshMixer | 2026-08-08 12:00:40 | 425 | ||||||||
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MareNostrum Resource Report Resource Website 1+ mentions |
MareNostrum (RRID:SCR_015737) | software resource | Operating software for a supercomputer in Spain. The software is maintained and updated by the Centro Nacional de Supercomputación (Barcelona Supercomputing Center) and is used for research projects on climate change, gravitational waves, a vaccination against AIDS, new radiation treatments to fight cancer, and other subjects. | supercomputer, operating system, petaflop, research project, research software | Available to affiliated researchers | SCR_015737 | 2026-08-08 12:00:43 | 6 | |||||||||||
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ReMESH Resource Report Resource Website 1+ mentions |
ReMESH (RRID:SCR_015735) | authoring tool, 3d visualization software, software resource, software application, data visualization software, data processing software | 3D editing software for manifold triangle meshes with advanced repairing features. It can post-process polygon meshes coming from digitization sessions and automatically filter out most of the typical flaws that models may have when coming from a 3D digitization session (degenerate triangles, isolated vertices, noise, topological artefacts, holes, ...). | 3d mesh, 3d design, 3d visualization, polygon mesh, mesh repair, manifold triangle mesh, 3d editing, digitization | Free, Available for download, Runs on Windows, Runs on Linux, Acknowledgment requested | SCR_015735 | ReMESH - Edit and Repair Polygon Meshes | 2026-08-08 12:00:25 | 5 | ||||||||||
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RootTrace Resource Report Resource Website 1+ mentions |
RootTrace (RRID:SCR_015585) | software resource, software application, data analysis software, data processing software | Software tool which allows the automatic and high throughput measure of root length, as well as extra associated measures such as curvature. The user must supply start points for each root, and exemplar patches of nearby background. The software will then trace the main root to the tip, in every image in a timeseries, and record the results. | root length, root measurement, plant root, root bioinformatics | Available for download | SCR_015585 | 2026-08-08 12:00:38 | 3 | |||||||||||
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GRatio for ImageJ Resource Report Resource Website 10+ mentions |
GRatio for ImageJ (RRID:SCR_015580) | software resource, software application, source code, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 5,2026.ImageJ plugin that performs semiautomated analysis of randomly selected sets of nervous system fibers. | myelin sheath, axon diameter, fiber diameter, g ratio, plugin | is a plug in for: ImageJ | neurodegeneration | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015580 | GRatio | 2026-08-08 12:00:38 | 30 | ||||||||
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Cerebrovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cerebrovascular Disease Knowledge Portal (RRID:SCR_015628) | CDKP | data or information resource, topical portal, database, portal, disease-related portal | Portal enables browsing, searching, and analysis of human genetic information linked to cerebrovascular disease and related traits, while protecting the integrity and confidentiality of the underlying data. | human, genetic, information, cerebrovascular, disease, data, knowledge |
is listed by: NIDDK Information Network (dkNET) has parent organization: Massachusetts General Hospital Labs and Facilities |
cerebrovascular disease | NINDS ; NIH ; Accelerating Medicines Partnership in Type 2 Diabetes |
Free, Available for download | SCR_016535 | SCR_015628 | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-08-08 12:00:38 | 17 | |||||
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BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | web application, software resource, software application, data visualization software, data processing software | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
Wellcome Trust ; WTCCB ; ERC ; Genome Québec International Recruitment Award |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-08-08 12:00:41 | 370 | ||||||
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primers4clades Resource Report Resource Website 1+ mentions |
primers4clades (RRID:SCR_015714) | web application, software resource | Web application for the design of PCR primers for cross-species amplification of novel sequences from metagenomic DNA or from uncharacterized organisms belonging to user-specified phylogenetic lineages. It implements an extended CODEHOP strategy and evaluates thermodynamic properties of the oligonucleotide pairs. | pcr primer, metagenomic dna, phylogenetic lineage, primer, clade, bio.tools |
is listed by: Debian is listed by: bio.tools |
DGAPA IN201806-2; CONACyT-Mexico P1-60071; CSIC 200720I038 |
PMID:19465390 | Freely available, Free for academic use, Tutorial available | biotools:primers4clades | http://maya.ccg.unam.mx/primers4clades, https://bio.tools/primers4clades | SCR_015714 | 2026-08-08 12:00:43 | 2 | ||||||
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ARCHS4 Resource Report Resource Website 50+ mentions |
ARCHS4 (RRID:SCR_015683) | software tool | ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome. | SCR_015683 | 2026-08-08 12:00:42 | 84 | |||||||||||||
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Cuffmerge Resource Report Resource Website 500+ mentions |
Cuffmerge (RRID:SCR_015688) | software tool | The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53. | SCR_015688 | 2026-08-08 12:00:25 | 951 | |||||||||||||
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clustergrammer Resource Report Resource Website 10+ mentions |
clustergrammer (RRID:SCR_015681) | software tool, data visualization tool | Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features. | bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/sdata.2017.151 | biotools:clustergrammer | https://bio.tools/clustergrammer | SCR_015681 | 2026-08-08 12:00:25 | 48 | ||||||||
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Dynamic Spatial Illuminator Software Resource Report Resource Website 1+ mentions |
Dynamic Spatial Illuminator Software (RRID:SCR_015725) | software resource | Software used in tandem with the Polygon 400 from Mightex systems to define areas of illumination, control light intensity and duration, and calibrate the device. | illumination, light intensity, device calibration, mightex system, polygon 400, spatial resolution | Commercially available, Available for purchase | http://www.mightexsystems.com/family_info.php?cPath=245_347_346&categories_id=346 | SCR_015725 | 2026-08-08 12:00:43 | 1 | ||||||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | software resource, software application, source code, data analysis software, data processing software | Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files). | oligonucleotide, microarray gene expression, r, oligonucleotide array, snp, gene expression, probe-level, affymetrix array, cel file, and nimblegen array, xys file, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
CAPES (Coordenação de Aprimoramento Pessoal de Nível Superior) ; NCRR R01RR021967; NHGRI P41HG004059 |
PMID:20688976 | Free, Available for download, Runs on Mac OS, Runs on Windows | biotools:oligo | https://bio.tools/oligo | SCR_015729 | oligo package | 2026-08-08 12:00:40 | 1808 | |||||
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BSVF Resource Report Resource Website 1+ mentions |
BSVF (RRID:SCR_015727) | BSVF | sequence analysis software, software resource, software application, source code, data analysis software, data processing software | Software code for bisulfite sequencing virus integration. This finder is for directional libraries only and does not support PBAT and indirectional libraries. | virus integration, sequencing analysis, virus assembly, integration, bisulfite, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:bs-virus-finder | https://bio.tools/bs-virus-finder | SCR_015727 | BSVF: Bisulfite Sequencing Virus integration Finder, Bisulfite Sequencing Virus integration Finder | 2026-08-08 12:00:25 | 1 |
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