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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data or information resource, database, service resource, storage service resource, data repository | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NSF EF0843229; NIGMS U24 GM144232 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-08-08 11:58:49 | 15 | ||||
|
EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-08-08 11:59:02 | 20 | |||||
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Cancer Cell Map Resource Report Resource Website 10+ mentions |
Cancer Cell Map (RRID:SCR_006792) | Cancer Cell Map | data or information resource, production service resource, web service, software resource, data analysis service, data access protocol, database, analysis service resource, service resource | It is a collection of selected human-focused cellular pathways implicated in cancer that are linked to visualization and analysis tools. Biologists can browse and search the Cancer Cell Map pathways and view gene expression data on any pathway. All data is freely available. Computational biologists can download all pathways in BioPAX format for global analysis. Software developers can build software on top of the Cancer Cell Map using the web service API. Download and install the cPath pathway database software to create a local mirror of the Cancer Cell Map. Cancer Cell Map pathways were selected based on the scientific interests of research labs at Memorial Sloan-Kettering Cancer Center. Effort was made not to duplicate information in other public pathway databases. Available pathways include: Alpha6Beta4Integrin, AndrogenReceptor, EGFR1, Hedgehog, ID, KitReceptor, NOTCH, TGFBR, TNF alpha/NF-kB, Wnt. Each pathway has around 100-400 interactions. | cancer, cell map, cellular, human cancer pathway, homo sapiens, mus musculus, rattus norvegicus | is related to: Pathway Commons | nif-0000-20919 | SCR_006792 | The Cancer Cell Map | 2026-08-08 11:58:42 | 21 | ||||||||
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Pel-Freez Biologicals Resource Report Resource Website 100+ mentions |
Pel-Freez Biologicals (RRID:SCR_006827) | commercial organization | An Antibody supplier | nlx_152427 | SCR_006827 | Pel-Freez | 2026-08-08 11:58:50 | 143 | |||||||||||
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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 | |||||||||||
|
Harvard Digestive Disease Center Resource Report Resource Website |
Harvard Digestive Disease Center (RRID:SCR_015587) | HDDC | data or information resource, topical portal, portal, organization portal, disease-related 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 | 2026-08-08 12:00:41 | 0 | |||||||
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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 | |||||
|
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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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 | Glo Max Multi Detection System, GloMax Multi Detection System | 2026-08-08 12:00:41 | 9 |
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