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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UAMH Centre for Global Microfungal Biodiversity Resource Report Resource Website 1+ mentions |
UAMH Centre for Global Microfungal Biodiversity (RRID:SCR_016466) | biomaterial supply resource, material resource, organism supplier | Repository of microbial in Canada. Culture collection, preservation, analysis, identification of fungi living strains. Backed up by herbarium dried colonies. A reference and training centre for the identification of human and animal pathogens and allied taxa.Provides advice or assistance to projects involving fungi. | microbial, repository, collection, preservation, analysis, identification, fungi | is related to: University of Toronto; Ontario; Canada | SCR_016466 | 2026-09-03 04:53:38 | 5 | |||||||||||
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, database, organism-related portal, portal, topical portal | 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 13th Five-year Informatization Plan 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 National Science Foundation for Young Scientists of China ; the Strategic Priority Research Program of the Chinese Academy of Sciences |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-09-03 04:53:50 | 5 | |||||
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iMaps Resource Report Resource Website 10+ mentions |
iMaps (RRID:SCR_016705) | analysis service resource, data analysis service, data or information resource, portal, production service resource, 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 | 2026-09-03 04:54:00 | 11 | ||||||||||
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Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | 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 | 2026-09-03 04:53:58 | 33 | ||||||
|
iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data analysis software, data processing software, software application, 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 | 2026-09-03 04:54:01 | 39 | |||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data analysis software, data processing software, data visualization software, image analysis software, software application, software resource | 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 | 2026-09-03 04:53:54 | 5 | ||||||
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BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | data analysis software, data processing software, data visualization software, software application, software resource | Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems. | control, cell, sorter, acquisition, analysis, integrate, data, instrument, system, Becton Dickinson and Company | Commercially available | SCR_016722 | , BD FACS Sortware, Becton Dickinson FACS Sortware, BD FACS Sortware software | 2026-09-03 04:54:00 | 5 | |||||||||
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fermi Resource Report Resource Website |
fermi (RRID:SCR_016652) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes. | assembler, analysis, whole, genome, short, gun, sequencing, error, correction | is listed by: OMICtools | NHGRI U01 HG005208 | PMID:22569178 | Free, Available for download, Freely available | SCR_016652 | 2026-09-03 04:53:56 | 0 | ||||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | data analysis software, data processing software, software application, software resource, software toolkit | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-09-03 04:54:51 | 6 | |||||||||||
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Vesselucida Explorer Resource Report Resource Website 1+ mentions |
Vesselucida Explorer (RRID:SCR_017674) | data analysis software, data processing software, software application, software resource | Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more. | MBF Bioscience, analysis, vasculature, specific, metric, segment, node, count, frequency, anastomoses, vessel, surface, volume | works with: Vesselucida 360 | Restricted | SCR_017674 | 2026-09-03 04:54:32 | 2 | ||||||||||
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fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | data analysis software, data processing software, software application, software resource | Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data. | Identifying population structure, dense sequencing data, Bayesian clustering, large dataset, data, analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:finestructure | https://bio.tools/finestructure | SCR_018170 | FineSTRUCTURE version 2 | 2026-09-03 04:55:02 | 23 | |||||||
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SAVES Resource Report Resource Website 100+ mentions |
SAVES (RRID:SCR_018219) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server. | Structure validation, homology modeling, obtained model, analysis, validation server | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018219 | SAVES v5.0, Structure Analysis and Verification Server | 2026-09-03 04:54:56 | 219 | |||||||||
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ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling. | Chromatin loop, CHi-C promoter, data, Hi-C visualization, interaction calling, data, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31118054 | Free, Freely available | biotools:ChiCMaxima | https://bio.tools/ChiCMaxima | SCR_018178 | 2026-09-03 04:54:54 | 2 | |||||||
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SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | data analysis software, data processing software, software application, software resource | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; European Research Council ; Wellcome Trust |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-09-03 04:54:53 | 3 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | data analysis software, data processing software, software application, software resource | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; European Research Council ; Royal Society ; Wellcome Trust |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-09-03 04:54:59 | 1 | ||||||||
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MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | data analysis software, data processing software, software application, software resource | Software package for motion capture analysis by Innovision Systems Inc. | Motion capture, analysis, data, data tracking, Innovision Systems Inc. | Restricted | SCR_018188 | Innovision Systems MaxTRAQ software | 2026-09-03 04:54:45 | 2 | ||||||||||
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NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | analysis service resource, data analysis service, data or information resource, portal, production service resource, service resource, topical portal | Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools. | Visualization, analysis, multi omic data, cell type, developing brain, adult brain, RNAseq, ATACseq, CHIPseq, fetal human prefrontal cortex, stem cell, neural induction, brain, data |
is used by: BICCN is related to: NeMOarchive is related to: BRAIN Initiative is related to: Brainome portal is related to: BRAIN Initiative Cell Atlas Network |
Free, Freely available | SCR_018244 | SCR_018164 | Neuroscience Multi-Omic Analytics | 2026-09-03 04:54:58 | 16 | ||||||||
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ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-09-03 04:54:43 | 50 | ||||||
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gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | data analysis software, data processing software, software application, software resource | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | gprofiler2 | 2026-09-03 04:55:03 | 63 | |||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | data analysis software, data processing software, software application, software resource, software toolkit | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | Quantify unknown Biophysics | 2026-09-03 04:54:50 | 2 |
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