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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | database, web service, data or information resource, data access protocol, software resource | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-08-14 09:28:02 | 317 | |||||||
|
D-GENIES Resource Report Resource Website 50+ mentions |
D-GENIES (RRID:SCR_018967) | standalone software, image analysis software, data processing software, web application, software application, software resource, alignment software | Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. | bio.tools |
uses: Minimap2 is listed by: Debian is listed by: bio.tools |
PMID:29888139 | Free, Available for download, Freely available | biotools:d-genies | https://github.com/genotoul-bioinfo/dgenies, https://bio.tools/d-genies | SCR_018967 | Dot plot large GENomes in an Interactive, Efficient and Simple way | 2026-08-14 09:28:01 | 56 | ||||||
|
PhyloPic Resource Report Resource Website 500+ mentions |
PhyloPic (RRID:SCR_019139) | data repository, storage service resource, web service, data access protocol, data or information resource, software resource, service resource | Silhouette images of animals, plants, and other life forms, available for reuse. Database stores reusable silhouette images and phylogenetic taxonomy of all organisms. Each image is associated with one or more taxonomic names and indicates roughly what ancestral member of each taxon looked like. | Silhouette images, phylogenetic taxonomy, taxonomic name, taxon ancestral member, supertaxa, subtaxa, image related taxa, FASEB list | Free, Freely available | SCR_019139 | 2026-08-14 09:28:12 | 714 | |||||||||||
|
BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | data processing software, software application, data analysis software, software resource | Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data. | Biosynthetic Gene, gene clusters, super linear clustering, clustering data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Graduate School for Experimental Plant Sciences Netherlands |
DOI:10.1101/2020.08.17.240838 | Free, Available for download, Freely available | biotools:big_slice | https://bio.tools/big_slice | SCR_019130 | Biosynthetic Gene clusters - Super Linear Clustering Engine | 2026-08-14 09:28:04 | 6 | |||||
|
PROSPERO Resource Report Resource Website 1000+ mentions |
PROSPERO (RRID:SCR_019061) | data or information resource, database, standard specification, narrative resource | International database of prospectively registered systematic reviews in health and social care, welfare, public health, education, crime, justice, and international development, where there is health related outcome. Key features from review protocol are recorded and maintained as permanent record. Aims to provide comprehensive listing of systematic reviews registered at inception to help avoid duplication and reduce opportunity for reporting bias by enabling comparison of completed review with what was planned in protocol. | Gold standard authority, registered systematic reviews, reviews in health, reviews in social care, reviews in welfare, reviews in public health, reviews in education, reviews in crime, reviews in justice, reviews in international development, health related outcome, protocol, FASEB list |
is related to: Centre for Reviews and Dissemination has parent organization: University of York, York, England |
NIHR | Free, Freely available | SCR_019061 | 2026-08-14 09:28:03 | 3301 | |||||||||
|
COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | topical portal, disease-related portal, data repository, storage service resource, portal, data or information resource, service resource | Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings. | COVID-19, impact data, novel coronavirus global pandemic, novel coronavirus, data |
uses: DataCite is related to: OpenICPSR has parent organization: University of Michigan; Ann Arbor; USA |
COVID-19 | Free, Freely available | https://doi.org/10.3886, https://dx.doi.org/10.3886 | SCR_019105 | 2026-08-14 09:28:11 | 1 | ||||||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | software toolkit, data processing software, software application, data analysis software, software resource | Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data. | structural variants identification, reference genome, structural variant calls generation, whole genome sequencing data, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parliament2 | https://bio.tools/parliament2 | SCR_019187 | 2026-08-14 09:28:06 | 5 | ||||||||
|
NEMAR Resource Report Resource Website 1+ mentions |
NEMAR (RRID:SCR_019100) | data or information resource, portal, topical portal | Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource. | Human electrophysiological data, neuroelectromagnetic data, neuroelectromagnetic tools, data archives, data analysis, data visualization, EEG data, MEG data, iEEG data, ECoG data, brain data | is affiliated with: OpenNeuro | NIH | Free, Freely available | SCR_019100 | NEuroelectroMagnetic data Archive and tools Resource | 2026-08-14 09:28:03 | 9 | ||||||||
|
CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data processing software, web service, data access protocol, software application, software resource, data visualization software | Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. | Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification | Nine Girls Ask Foundation ; NCI CA207729; NIGMS GM132055; NCI CA107263; NCI CA177519; NCI CA102310; NIA AG033082; NCI P30 CA138313 |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2026-08-14 09:28:26 | 0 | |||||||
|
Computational Anatomy Toolbox for SPM Resource Report Resource Website 500+ mentions |
Computational Anatomy Toolbox for SPM (RRID:SCR_019184) | CAT | software toolkit, data processing software, software application, data analysis software, software resource | Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry. | MRI, neuroimaging, brain, voxel based morphometry, surface based morphometry, deformation based morphometry, label based morphometry, region based morphometry | works with: SPM | Free, Available for download, Freely available | SCR_019184 | CAT12 | 2026-08-14 09:28:27 | 581 | ||||||||
|
Scayle Resource Report Resource Website |
Scayle (RRID:SCR_019064) | data repository, storage service resource, portal, data or information resource, data set, spatially referenced dataset, service resource, atlas | Open source data platform and multidisciplinary online repository where research groups and different organizations store and make public their datasets, managed by Scayle. Collection of public datasets are available through open.scayle.es and can be reused. NetFlow is network protocol developed by Cisco for collection and monitoring of network traffic flow data generated. Netflow datasets have been used to train machine learning models. | Netflow, DOROTHEA, dataset, network traffic, port scan, training data, traffic flow data | has parent organization: University of Leon, Spain | Free, Freely available, Available for download | https://open.scayle.es/dataset, https://open.scayle.es/dataset/netflow-data-with-sampling-for-test, https://open.scayle.es/dataset/netflow-data-with-sampling-for-training | https://open.scayle.es/dataset/netflow-data, https://open.scayle.es/dataset/netflow-data-without-sampling | SCR_019064 | open.scayle.es | 2026-08-14 09:28:11 | 0 | |||||||
|
tidyverse Resource Report Resource Website 100+ mentions |
tidyverse (RRID:SCR_019186) | software toolkit, data processing software, software application, data analysis software, software resource | Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses. | data science, R package, data analysis, common data representation |
uses: ggplot2 uses: dplyr uses: tidyr is used by: tidySingleCellExperiment is used by: microViz is listed by: CRAN |
Free, Available for download, Freely available | https://www.tidyverse.org/, https://github.com/tidyverse/tidyverse | SCR_019186 | tidyverse 1.3.0 | 2026-08-14 09:28:13 | 259 | ||||||||
|
UCSC Xena Resource Report Resource Website 1000+ mentions |
UCSC Xena (RRID:SCR_018938) | production service resource, portal, web service, data or information resource, data access protocol, software resource, service resource, analysis service resource | Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. | Data visualization, data analysis, genomics data, explore functional genomic data, functional genomic, data sets, genomic variable correlation, phenotypic variables correlation | has parent organization: University of California at Santa Cruz; California; USA | Free, Freely available | https://xenabrowser.net/ | SCR_018938 | UCSC Xena Browser, Xena Browser | 2026-08-14 09:28:08 | 4804 | ||||||||
|
Network-Based R-Statistics Resource Report Resource Website 1+ mentions |
Network-Based R-Statistics (RRID:SCR_019114) | NBR | software toolkit, data processing software, software application, data analysis software, network analysis software, software resource | Software tool as implementation of network based statistics toolbox in R. Includes mixed effects models. | Network based statistics, R, mixed effects model |
is listed by: CRAN is related to: Network Based Statistic Toolbox is related to: R Project for Statistical Computing |
Free, Freely available | SCR_019114 | 2026-08-14 09:28:12 | 3 | |||||||||
|
long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | data or information resource, software repository, software resource, database | Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies. | Software tools collection, long read sequencing data, long read sequencing, data analysis, data analysis tools, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:32033565 | Free, Freely available | biotools:long-read-tools | https://github.com/shaniAmare/long_read_tools, https://bio.tools/long-read-tools | SCR_019116 | Long-Read-Tools, long-read-tools.org | 2026-08-14 09:28:26 | 14 | ||||||
|
BioSimulators Resource Report Resource Website 1+ mentions |
BioSimulators (RRID:SCR_019111) | software repository, web application, software resource | Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects. | Containerized biosimulation tools, consistent interfaces, choosing simulator guide, supported modeling frameworks, simulation algorithms, modeling formats, bio.tools |
is used by: runBioSimulations is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; National Institutes of Health ; National Science Foundation |
Free, Freely available | biotools:biosimulators | https://bio.tools/biosimulators | SCR_019111 | 2026-08-14 09:28:04 | 5 | |||||||
|
AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | data processing software, software application, software resource, workflow software | Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications. | High Performance Computing, HPC environment, rRNA gene amplicons, rRNA marker, gene amplicon pipeline, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:31816087 | Free, Freely available | SCR_019113, biotools:amplicontagger | https://bitbucket.org/jtremblay514/nrc_pipeline_public/src/master/, https://jtremblay.github.io/amplicontagger_guide.html, https://bio.tolols/amplicontagger | SCR_019112 | 2026-08-14 09:28:26 | 3 | |||||||
|
o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | software application, simulation software, software resource | Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response. | SPARC, SPARC computational model, data sharing, model coupling, cloud based execution, data visualization, data analysis, peripheral nervous system, organ functional response |
is used by: SPARC Portal is organization facet of: SPARC Portal |
Free, Freely available | SCR_018997 | open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions | 2026-08-14 09:28:02 | 2 | ||||||||
|
Numbat Resource Report Resource Website 10+ mentions |
Numbat (RRID:SCR_019207) | software application, software resource, data management software | Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context. | Manage large references databases, large data, manage different extraction levels, multiple extraction forms, codebooks, reference network generation, publication database, systematic review, academic context | Free, Available for download, Freely available | https://github.com/bgcarlisle/Numbat, https://numbat.bgcarlisle.com | SCR_019207 | Numbat Systematic Review Manager | 2026-08-14 09:28:06 | 11 | |||||||||
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variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data processing software, software application, data analysis software, data analytics software, software resource | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
NHLBI U01 HL107388; Icahn School of Medicine at Mount Sinai |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-08-14 09:28:28 | 62 |
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