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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ReMESH Resource Report Resource Website 1+ mentions |
ReMESH (RRID:SCR_015735) | 3d visualization software, authoring tool, data processing software, data visualization software, software application, software resource | 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 | SciCrunch Registry | ReMESH - Edit and Repair Polygon Meshes | 2026-11-07 11:58:28 | 5 | ||||||||||
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RootTrace Resource Report Resource Website 1+ mentions |
RootTrace (RRID:SCR_015585) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-11-07 11:58:12 | 3 | |||||||||||
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SpiCoDyn Resource Report Resource Website 1+ mentions |
SpiCoDyn (RRID:SCR_015744) | data analysis software, data processing software, software application, software resource, source code | Software for the analysis of multi-site neuronal spike signals. SPICODYN processes electrophysiological signals, focusing on spiking and bursting dynamics and functional-effective connectivity analysis. | spike signal, neuron, multi-site neuronal spike signal, eeg, electrophysiology, brain imaging | Open source, Available for download | SCR_015744 | SciCrunch Registry | 2026-11-07 11:58:04 | 2 | |||||||||||
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Harvard Digestive Disease Center Resource Report Resource Website |
Harvard Digestive Disease Center (RRID:SCR_015587) | HDDC | data or information resource, disease-related portal, organization portal, portal, topical portal | Community of scientists focused on the study of epithelial cell function and mucosal biology including inflammation and host defense of the gastrointestinal tract. It focuses on the intestinal and inflammatory bowel diseases; gut microbiology; and stem cell and developmental biology of the intestine and liver in organ physiology, regenerative medicine, and metabolism. | digestive disease, inflammatory bowel disease, epithelial cell function, mucosal biology, inflammation, stem cell biology |
is listed by: NIDDK Information Network (dkNET) has parent organization: Harvard University; Cambridge; United States is parent organization of: Harvard Digestive Diseases Center Biomedical CORE B: Microscopy and Histopathology is parent organization of: Harvard Digestive Diseases Center Biomedical CORE C: Epithelial Cell and Mucosal Immunology is parent organization of: Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics is parent organization of: Harvard Digestive Diseases Center Clinical Translational Research Program is parent organization of: Harvard Digestive Diseases Center Bio-Repository and Data Registry for Human Material has organization facet: Harvard Digestive Diseases Center Biomedical CORE B: Microscopy and Histopathology has organization facet: Harvard Digestive Diseases Center Biomedical CORE C: Epithelial Cell and Mucosal Immunology has organization facet: Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics has organization facet: Harvard Digestive Diseases Center Clinical Translational Research Program has organization facet: Harvard Digestive Diseases Center Bio-Repository and Data Registry for Human Material is organization facet of: Digestive Disease Centers |
digestive disease, Inflammatory Bowel Disease, | NIDDK P30 DK034854 | Available to the research community | SCR_015587 | SciCrunch Registry | 2026-11-07 11:58:26 | 0 | |||||||
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GRatio for ImageJ Resource Report Resource Website 10+ mentions |
GRatio for ImageJ (RRID:SCR_015580) | data analysis software, data processing software, software application, software resource, source code | 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 | SciCrunch Registry | GRatio | 2026-11-07 11:58:26 | 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, database, disease-related portal, portal, topical 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 | Accelerating Medicines Partnership in Type 2 Diabetes ; NIH ; NINDS |
Free, Available for download | SCR_016535 | SCR_015628 | SciCrunch Registry | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-11-07 11:58:26 | 17 | |||||
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PISA Resource Report Resource Website 1000+ mentions |
PISA (RRID:SCR_015749) | PDBePISA | software resource, web application | Web application for exploration of macromolecular interfaces. It calculates structural and chemical properties of macromolecular surfaces and interfaces, as well as quaternary structures (assemblies), their structural and chemical properties and dissociation patterns. | macromolecule, assembly, dissociation pattern, chemical composition | BBSRC 721/B19544 | PMID:17681537 | Freely available, Free, Available for download, Tutorial available | SCR_015749 | SciCrunch Registry | PDBePISA, Proteins Interfaces Structures and Assemblies | 2026-11-07 11:58:28 | 1638 | |||||||
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BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | data processing software, data visualization software, software application, software resource, web application | 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 |
ERC ; Genome Québec International Recruitment Award ; Wellcome Trust ; WTCCB |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | SciCrunch Registry | 2026-11-07 11:58:28 | 370 | ||||||
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CNVcaller Resource Report Resource Website 10+ mentions |
CNVcaller (RRID:SCR_015752) | CNVcaller | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Software for detecting the integrated copy number variation regions (CNVRs) using population sequencing data. The high-confidence CNVRs are discovered and refined by both individual and population criteria, and the result is a VCF format genotype file which can be used in GWAS/QLT research. | copy number variation, cnv, next-generation sequencing, ngs, population genetic, segmental duplication, absolute copy number | Free, Available for download | SCR_015752 | SciCrunch Registry | 2026-11-07 11:58:05 | 40 | ||||||||||
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primers4clades Resource Report Resource Website 1+ mentions |
primers4clades (RRID:SCR_015714) | software resource, web application | 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 | SciCrunch Registry | 2026-11-07 11:58:14 | 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 | SciCrunch Registry | 2026-11-07 11:58:03 | 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 | SciCrunch Registry | 2026-11-07 11:58:04 | 951 | |||||||||||||
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clustergrammer Resource Report Resource Website 10+ mentions |
clustergrammer (RRID:SCR_015681) | data visualization tool, software 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 | SciCrunch Registry | 2026-11-07 11:58:27 | 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 | SciCrunch Registry | 2026-11-07 11:58:30 | 1 | ||||||||||
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oligo Resource Report Resource Website 1000+ mentions |
oligo (RRID:SCR_015729) | data analysis software, data processing software, software application, software resource, source code | 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 | SciCrunch Registry | oligo package | 2026-11-07 11:58:14 | 1808 | |||||
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BSVF Resource Report Resource Website 1+ mentions |
BSVF (RRID:SCR_015727) | BSVF | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | 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 | SciCrunch Registry | BSVF: Bisulfite Sequencing Virus integration Finder, Bisulfite Sequencing Virus integration Finder | 2026-11-07 11:58:04 | 1 | ||||||
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Glo-Max Multi Detection System Resource Report Resource Website 1+ mentions |
Glo-Max Multi Detection System (RRID:SCR_015575) | resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 6, 2017. Detection instrument that gathers absorbance, fluorescence, and luminescence data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | detection instrument, absorbance machine, fluorescence machine, luminescence machine, hardware, instrument, equipment | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015575 | SciCrunch Registry | Glo Max Multi Detection System, GloMax Multi Detection System | 2026-11-07 11:58:02 | 9 | ||||||||||
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Torrent Variant Caller Standalone Resource Report Resource Website 10+ mentions |
Torrent Variant Caller Standalone (RRID:SCR_015694) | software tool | A variant vcf file analysis tool. | http://updates.iontorrent.com/tvc_standalone/ | SCR_015694 | SciCrunch Registry | 2026-11-07 11:58:13 | 41 | ||||||||||||
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GenePattern Notebook Resource Report Resource Website 1+ mentions |
GenePattern Notebook (RRID:SCR_015699) | electronic laboratory notebook, software application, software resource, systems interoperability software, web application | Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code. | gene, genomics research, research narrative, notebook system, analysis notebook, bio.tools |
is listed by: bio.tools is listed by: Debian is affiliated with: GenePattern |
NIGMS R01-GM074024; NCI U24-CA194107 |
PMID:28822753 | Open Source, Free, Available for download, Account required | biotools:GenePattern_notebook | https://bio.tools/GenePattern_notebook | SCR_015699 | SciCrunch Registry | GenePattern Notebook environment | 2026-11-07 11:58:04 | 3 | |||||
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University of Pennsylvania Diabetes Research Center Resource Report Resource Website 1+ mentions |
University of Pennsylvania Diabetes Research Center (RRID:SCR_015732) | DRC | data or information resource, disease-related portal, portal, topical portal | NIDDK center that serves diabetes-oriented investigators from University of Pennsylvania as well as additional institutions from the mid-Atlantic region. The Penn DRC represents many basic science and clinical departments at Penn and the other institutions, and supports research in diabetes and obesity via Scientific Cores, a Pilot and Feasibility Grant Program, and a series of seminars, retreats, and other academic enrichment activities. | diabetes, research, univeristy of pennsylvania, upenn, obesity, metabolic disorder | is listed by: NIDDK Information Network (dkNET) | NIDDK P30DK19525 | Available to affiliated researchers | http://www.med.upenn.edu/, https://diabetescenters.org/ | SCR_015732 | SciCrunch Registry | 2026-11-07 11:58:04 | 1 |
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