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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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datasets.datalad.org Resource Report Resource Website 1+ mentions |
datasets.datalad.org (RRID:SCR_019089) | data or information resource, service resource, data repository, storage service resource, data set | DataLad data distribution. Super dataset collating DataLad datasets from various sources including OpenNeuro, CRCNS, etc., to provide unified access to over 200TB of neural data. | Version control system, data distribution, super dataset, DataLad dataset, neural data | is related to: DataLad | NSF 1429999; NSF 1912266; NIBIB P41 EB019936 |
Free, Freely available | https://www.datalad.org/datasets.html | SCR_019089 | 2026-08-13 09:30:19 | 8 | ||||||||
|
HADDOCK Resource Report Resource Website 100+ mentions |
HADDOCK (RRID:SCR_019091) | data access protocol, simulation software, software application, web service, software resource | Software tool as information driven flexible docking approach for modeling of biomolecular complexes.User friendly integrative modeling of biomolecular complexes.HADDOCK v 2.2 offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in user friendly interface. | Molecular docking, data driven, biomolecular complex, grid computing, hybrid modeling, protein complex | has parent organization: Utrecht University; Utrecht; Netherlands | PMID:12580598 PMID:26410586 |
Restricted | https://www.bonvinlab.org/software/haddock2.2/, https://wenmr.science.uu.nl/haddock2.4/ | SCR_019091 | HADDOCK2.2, HADDOCK2.4, High Ambiguity Driven protein-protein DOCKing | 2026-08-13 09:30:14 | 168 | |||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data or information resource, data access protocol, database, web service, 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 | 2026-08-13 09:30:18 | 317 | |||||||
|
Hiroshima University Amphibian Research Center Resource Report Resource Website 10+ mentions |
Hiroshima University Amphibian Research Center (RRID:SCR_019015) | ARC, HUARC | biomaterial supply resource, material resource, organism supplier | Stock center that provides amphibian organisms, frogs and newts, primarily to Japanese investigators. The center runs the National BioResource Project (NBRP) Clawed frogs / Newts, which is financially supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan, to distribute these resources. Contributes to maintenance of biologically important strains of frogs and study biological characteristics of amphibian focusing genetics, developmental regulation, speciation, phylogeny, phenotype expression, and environment-induced mutagenesis. | Amphibian, Frog, Xenopus, Newt, Hiroshima University | Ministry of Education ; Culture ; Sports ; Science and Technology (MEXT) |
https://xenopus.nbrp.jp/NBRP_Xenopus/NBRP_X._tropicalis_Top_Page_EN.html | SCR_019015 | Amphibian Research Center, Institute for Amphibian Biology | 2026-08-13 09:30:18 | 10 | ||||||||
|
PhyloPic Resource Report Resource Website 500+ mentions |
PhyloPic (RRID:SCR_019139) | data or information resource, data access protocol, service resource, data repository, web service, storage service resource, software 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 | 2026-08-13 09:30:36 | 714 | |||||||||||
|
BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | data analysis software, data processing software, software resource, software application | 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 | 2026-08-13 09:30:36 | 6 | |||||
|
COVID-19 Data Repository Resource Report Resource Website 1+ mentions |
COVID-19 Data Repository (RRID:SCR_019105) | topical portal, data or information resource, disease-related portal, service resource, data repository, storage service resource, portal | 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 | 2026-08-13 09:30:15 | 1 | ||||||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | data analysis software, data processing software, software application, software toolkit, 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 | 2026-08-13 09:30:36 | 5 | ||||||||
|
NEMAR Resource Report Resource Website 1+ mentions |
NEMAR (RRID:SCR_019100) | topical portal, data or information resource, 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 | 2026-08-13 09:30:15 | 9 | ||||||||
|
ABF Utility Resource Report Resource Website 1+ mentions |
ABF Utility (RRID:SCR_019222) | data analysis software, data processing software, software resource, software application | Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program. | Convert data file, ABF format, data file, data format | Restricted | SCR_019224 | SCR_019222 | 2026-08-13 09:30:37 | 4 | ||||||||||
|
OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | data acquisition software, data processing software, software resource, software application | Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system. | Clinical trial, data management system, clinical trial management system, clinical data, clinical data management | is listed by: SoftCite | PMID:21893916 | Restricted | https://www.openclinica.com/community-edition-open-source-edc/ | SCR_019223 | 2026-08-13 09:30:21 | 46 | ||||||||
|
Computational Anatomy Toolbox for SPM Resource Report Resource Website 500+ mentions |
Computational Anatomy Toolbox for SPM (RRID:SCR_019184) | CAT | data analysis software, data processing software, software application, software toolkit, 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 | 2026-08-13 09:30:21 | 581 | ||||||||
|
tidyverse Resource Report Resource Website 100+ mentions |
tidyverse (RRID:SCR_019186) | data analysis software, data processing software, software application, software toolkit, 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 | 2026-08-13 09:30:17 | 259 | ||||||||
|
Network-Based R-Statistics Resource Report Resource Website 1+ mentions |
Network-Based R-Statistics (RRID:SCR_019114) | NBR | data analysis software, data processing software, software application, software toolkit, 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 | 2026-08-13 09:30:15 | 3 | |||||||||
|
long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | data or information resource, database, software resource, software repository | 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 | 2026-08-13 09:30:20 | 14 | ||||||
|
BioSimulators Resource Report Resource Website 1+ mentions |
BioSimulators (RRID:SCR_019111) | web application, software resource, software repository | 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 | 2026-08-13 09:30:36 | 5 | |||||||
|
AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | workflow software, data processing software, software resource, software application | 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 | 2026-08-13 09:30:19 | 3 | |||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data analysis software, data processing software, software application, 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 | 2026-08-13 09:30:18 | 62 | ||||||
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Protein.Plus Resource Report Resource Website 50+ mentions |
Protein.Plus (RRID:SCR_019044) | data access protocol, software resource, web service | Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported. | Protein ligand interaction, protein structure, quality assessment, protein pocket detection, ensemble generation, metal coordinations prediction | has parent organization: University of Hamburg; Hamburg; Germany | Free, Freely available | SCR_019044 | 2026-08-13 09:30:19 | 59 | ||||||||||
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fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | data analysis software, data processing software, software application, time-series analysis software, 1d time-series analysis software, software resource | Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python. | Generalized linear model, hyperparameters, regularization technique, coefficient, linear regression, L2 norm, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:fracridge | https://bio.tools/fracridge | SCR_019045 | fractional ridge regression | 2026-08-13 09:30:14 | 1 |
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