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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Encode Resource Report Resource Website 1000+ mentions |
Encode (RRID:SCR_015482) | consortium, data or information resource, data set, organization portal, 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 | 2026-09-12 12:58:27 | 1293 | |||||||
|
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 | 2026-09-12 12:58:27 | 2 | ||||||||||
|
HISAT2 Resource Report Resource Website 10000+ mentions |
HISAT2 (RRID:SCR_015530) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | Graph-based alignment of next generation sequencing reads to a population of genomes. | alignment program, mapping reads, population genomics, human genome, bio.tools |
is used by: Fcirc is listed by: Debian is listed by: bio.tools is related to: TopHat has parent organization: Johns Hopkins University; Maryland; USA is required by: SL-quant is hosted by: GitHub |
NLM R01-LM06845; NIGMS R01-GM083873; NSF CCF-0347992 |
PMID:25751142 DOI:10.1038/s41587-019-0201-4 |
Available for download | OMICS_07225, biotools:hisat2 | https://github.com/infphilo/hisat2, https://bio.tools/hisat2, https://sources.debian.org/src/hisat2/ | SCR_015530 | HISAT | 2026-09-12 12:58:27 | 20753 | |||||
|
Platanus Resource Report Resource Website 100+ mentions |
Platanus (RRID:SCR_015531) | data analysis software, data processing software, sequence analysis software, software application, software resource | De novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo sequence assembly, genomic sequence reconstruction, shotgun sequence data | DOI:10.1101/gr.170720.113 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015531 | PLATform for Assembling NUcleotide Sequences, Platanus - PLATform for Assembling NUcleotide Sequences, Platanus Genome Assembler | 2026-09-12 12:58:27 | 201 | |||||||||
|
KZNF Catalog Resource Report Resource Website |
KZNF Catalog (RRID:SCR_015495) | catalog, data or information resource, database | Searchable, manually curated collection of Kruppel-type zinc finger genes (KZNFs) in primates with finished or high quality draft genomes. | kruppel type zinc finger gene, kznf, kruppel type zinc finger model, primate finger, primate finger gene | has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA | Open source | SCR_015495 | 2026-09-12 12:58:27 | 0 | ||||||||||
|
SEER Resource Report Resource Website 500+ mentions |
SEER (RRID:SCR_015499) | data analysis software, data processing software, sequence analysis software, software application, software resource, source code | 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 | 2026-09-12 12:58:27 | 547 | |||||||
|
MMPC-University of Michigan Medical School Resource Report Resource Website 1+ mentions |
MMPC-University of Michigan Medical School (RRID:SCR_015373) | access service resource, data or information resource, disease-related portal, portal, resource, service resource, topical 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 | 2026-09-12 12:58:26 | 1 | |||||||||
|
Autodesk Meshmixer Resource Report Resource Website 100+ mentions |
Autodesk Meshmixer (RRID:SCR_015736) | 3d visualization software, authoring tool, data processing software, data visualization software, software application, software resource | 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 | 2026-09-12 12:58:29 | 425 | ||||||||
|
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 | 2026-09-12 12:58:30 | 6 | |||||||||||
|
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 | ReMESH - Edit and Repair Polygon Meshes | 2026-09-12 12:58:29 | 5 | ||||||||||
|
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 | 2026-09-12 12:58:28 | 3 | |||||||||||
|
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 | 2026-09-12 12:58:30 | 2 | |||||||||||
|
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 | 2026-09-12 12:58:28 | 0 | |||||||
|
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 | GRatio | 2026-09-12 12:58:28 | 30 | ||||||||
|
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 | Cerebrovascular Disease Knowledge Portal (CDKP) | 2026-09-12 12:58:28 | 17 | |||||
|
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 | PDBePISA, Proteins Interfaces Structures and Assemblies | 2026-09-12 12:58:30 | 1638 | |||||||
|
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 | 2026-09-12 12:58:28 | 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 | 2026-09-12 12:58:30 | 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 | 2026-09-12 12:58:29 | 2 | ||||||
|
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 | 2026-09-12 12:58:29 | 84 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
