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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | software toolkit, data processing software, software application, data analysis software, software resource | Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. | geometric, morphometric, analyse, 2D, 3D, landmark, data, principal, component, discriminant, multivariate, regression, shape | has parent organization: University of Manchester; Manchester; United Kingdom | PMID:21429143 | Free, Available for download, Freely available | SCR_016483 | 2026-08-14 09:27:35 | 38 | |||||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software toolkit, data processing software, software application, data analysis software, software resource | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-08-14 09:27:33 | 2 | |||||
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NCBI Biocollections Resource Report Resource Website 1+ mentions |
NCBI Biocollections (RRID:SCR_016459) | NCBI Biocollections | database, image analysis software, data processing software, portal, registration software, data or information resource, software application, software resource, organization portal | Registry of bio-collections linked to genomes. Collection of curated dataset of metadata for culture collections, museums, herbaria and other natural history collections, including Darwin Core institution and collection codes, and URL formulae for mapping specimen ids to web pages at the collection site. | registry, biocollection, linked, genome, dataset, metadata | SCR_016459 | NCBI Biocollections:National Center for Biotechnology Information Biocollections | 2026-08-14 09:27:34 | 2 | ||||||||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | database, topical portal, organism-related portal, project portal, portal, web service, data or information resource, data access protocol, software resource | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | 2026-08-14 09:27:34 | 2 | |||||||||
|
masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | software toolkit, data processing software, software application, data analysis software, software resource | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-08-14 09:27:41 | 1 | ||||||
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MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-08-14 09:27:43 | 15 | ||||||
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cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | data processing software, software application, image processing software, software resource | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-08-14 09:27:25 | 67 | ||||
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LungMap Resource Report Resource Website 50+ mentions |
LungMap (RRID:SCR_016347) | LungMAP | data repository, storage service resource, portal, data or information resource, service resource | Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool. | lung, data, histochemistry, structural, molecular, normal, perinatal, postnatal, development, mouse, human, repository, images, transcriptomic, proteomic, lipidomic |
is related to: RTI International is related to: University of Texas at Austin; Texas; USA is related to: University of Alabama at Birmingham; Alabama; USA is related to: Yale University; Connecticut; USA is related to: University of California at San Diego; California; USA is related to: Carnegie Mellon University; Pennsylvania; USA is related to: Lung Genome Browser |
the National Heart ; Lung ; and Blood Institute of the National Institutes of Health U01HL122638 |
PMID:28798251 | Free, Freely available | SCR_016347 | The Molecular Atlas of Lung Development Program | 2026-08-14 09:27:33 | 68 | ||||||
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GCTF Resource Report Resource Website 100+ mentions |
GCTF (RRID:SCR_016500) | GCTF | data processing software, software application, data analysis software, software resource | Software tool as a Graphics Processing Units (GPU) accelerated computer program for real-time contrast transfer function (CTF) determination and correction. Used for a near-atomic resolution cryo electron microscopy (cryoEM) reconstruction to maximize the cross-correlation of a simulated CTF with the logarithmic amplitude spectra (LAS) of observed micrographs after background subtraction., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | accurate, real, time, constrast, transfer, function, determination, correction, atomic, resolution, cryo, electron, microscopy, reconstruction, micrograph | is related to: University of Cambridge; Cambridge; United Kingdom | the Medical Research Council ; United Kingdom MC_UP_A025_1011; Wellcome Trust New Investigator Award |
PMID:26592709 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016500 | GContrast Transfer Function | 2026-08-14 09:27:44 | 101 | ||||||
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MIRRI Resource Report Resource Website 10+ mentions |
MIRRI (RRID:SCR_016461) | MIRRI | database, topical portal, biobank, organism-related portal, storage service resource, portal, web service, data or information resource, data access protocol, software resource, service resource, organization portal, material storage repository, european biobank | Microbial stock center. Collaborative platform for the pan-European research infrastructure for microbial resources. Provides access to microorganisms, their derivatives, associated data and services for research, development and application. | European, research, infrastructure, microbial, resource, database, service, stock, center | the European Commission 312251; the European Union’s Seventh Framework Programme 312251 |
Free, Freely available | SCR_016461 | Microbal Resource Research Infrastructure | 2026-08-14 09:27:43 | 11 | ||||||||
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | database, topical portal, organism-related portal, portal, data or information resource | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the Strategic Priority Research Program of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-08-14 09:27:25 | 5 | |||||
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iMaps Resource Report Resource Website 10+ mentions |
iMaps (RRID:SCR_016705) | production service resource, data analysis service, portal, data or information resource, service resource, analysis service resource | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | 2026-08-14 09:27:28 | 11 | ||||||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | production service resource, data analysis service, web application, software resource, service resource, analysis service resource | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/, https://bio.tools/pavian | SCR_016679 | 2026-08-14 09:27:49 | 33 | ||||||
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iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data processing software, software application, data analysis software, software resource | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html, https://hub.docker.com/r/tomazc/icount/ | SCR_016712 | 2026-08-14 09:27:28 | 39 | |||||||||
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INC-Seq Resource Report Resource Website |
INC-Seq (RRID:SCR_016711) | INC-Seq | data processing software, software application, data analysis software, software resource, sequence analysis software | Software for accurate single molecule reads using nanopore sequencing. Used for 16S rRNA-based profiling to investigate complex bacterial communities. | accurate, single, molecule, read, nanopore, sequencing, 16S rRNA, bacteria | is related to: NanoAmpli-Seq | Agency for Science ; Technology and Research ; Singapore |
PMID:27485345 | Free, Available for download, Freely available | https://zenodo.org/record/57405#.W-nb0pNKiM8 | SCR_016711 | Intramolecular ligated Nanopore Consensus Sequencing, INC-Seq | 2026-08-14 09:27:37 | 0 | |||||
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NanoAmpli-Seq Resource Report Resource Website 1+ mentions |
NanoAmpli-Seq (RRID:SCR_016710) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing. | amplicon, sequencing, 16S rRNA, mixed, microbial, communities, nanopore, platform, gene |
is related to: INC-Seq has parent organization: University of Glasgow; Glasgow; United Kingdom |
EPSRC EP/M016811/1; NERC NE/L011956/1 |
DOI:10.1101/244517 | Free, Available for download, Freely available | https://www.protocols.io/view/nanoampli-seq-bioinformatics-workflow-u25eyg6 | SCR_016710 | 2026-08-14 09:27:49 | 1 | |||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | image analysis software, data processing software, software application, data analysis software, software resource, data visualization software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html, | SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-08-14 09:27:28 | 5 | ||||||
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Florida State University Physical Biochemistry Core Facility Resource Report Resource Website 1+ mentions |
Florida State University Physical Biochemistry Core Facility (RRID:SCR_016714) | PBF | core facility, production service resource, access service resource, availability annotation standard, standard specification, the community can contribute to this resource, training service resource, data or information resource, nif annotation standard, material service resource, service resource, narrative resource | Facility for biophysical studies of macromolecules with emphasis on providing resources, instrumentation, training, and guidance to graduate and undergraduate students. | core, facility, biophysical, study, macromolecule, providing, resource, instrument, training, guidance, student, Florida, State, University |
has parent organization: Florida State University; Florida; USA has parent organization: Institute of Molecular Biophysics at Florida State University; Florida; USA |
Restricted | SCR_016714 | The Physical Biochemistry Facility (PBF), The Physical Biochemistry Facility, Physical Biochemistry Facility | 2026-08-14 09:27:49 | 1 | ||||||||
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Stitching Resource Report Resource Website 1+ mentions |
Stitching (RRID:SCR_016568) | image analysis software, image processing software, data processing software, software application, software resource, image reconstruction software | Software package available through Fiji to image large biological specimen at high resolution. Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images. | biological, speciment, resoultion, reconstruct, big, image, stack, stitching | Free, Available for download, Freely available | https://github.com/fiji/Stitching/releases/tag/Stitching_-3.1.3 | SCR_016568 | 2026-08-14 09:27:36 | 4 | ||||||||||
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University of FLorida College of Medicine Molecular Pathology Core Facility Resource Report Resource Website 10+ mentions |
University of FLorida College of Medicine Molecular Pathology Core Facility (RRID:SCR_016601) | MPC | service resource, access service resource, core facility | Histology and light microscopy facility for paraffin and frozen blocks and all aspects of sample preparation, fixation, embedding, sectioning, staining, and imaging. Consultations, technical assistance and training are also provided. Standard operating procedures compliant with good laboratory and clinical processes are followed for all procedures. Services include cryosectioning, whole slide imaging, hematoxylin and eosin staining, immunfluorescence, and tissue microarrays.. | histology, immunohistochemistry, sample processing, clinical research, cryosectioning, imaging, staining, immunfluorescence, microarrays, core facility |
has parent organization: University of Florida Labs and Facilities has parent organization: University of Florida; Florida; USA |
Restricted | SCR_001055, SciEx_8810 | http://www.scienceexchange.com/facilities/molecular-pathology-core-ufl | SCR_016601 | Molecular Pathology Core, , University of Florida Molecular Pathology Core | 2026-08-14 09:27:27 | 17 |
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