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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | software application, web application, software resource, data processing software, data visualization software | 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 |
Wellcome Trust ; WTCCB ; ERC ; Genome Québec International Recruitment Award |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-07-28 09:43:57 | 360 | ||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | software application, data analysis software, sequence analysis software, software resource, data processing software, software toolkit | Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. | software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT098051; Alexander von Humboldt Stiftung/Foundation ; Medical Research Council G1100100/1 |
PMID:26794317 DOI:10.1093/bioinformatics/btw022 |
Free, Available for download, Freely available | OMICS_11083, biotools:bio-tradis | https://bio.tools/bio-tradis, https://sources.debian.org/src/bio-tradis/ | SCR_015993 | 2026-07-28 09:44:11 | 51 | |||||
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SC3 Resource Report Resource Website 10+ mentions |
SC3 (RRID:SCR_015953) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. | scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust 104710/Z/14/Z; Belgian Network DYSCO ; FRS-FNRS ; Belgian State Science Policy Office ; ARC (Action de Recherche Concerte) ; Wallonia-Brussels Federation ; EPSRC EP/N014529/1; Sanger Institute ; University of Edinburgh ; Bloodwise 13003; MRC ; Kay Kendall Leukaemia Fund ; Cambridge NIHR Biomedical Research Center ; Cambridge Experimental Cancer Medicine Centre ; Leukemia and Lymphoma Society of America 07037 |
PMID:28346451 | Free, Available for download | biotools:sc3 | https://bio.tools/sc3 | SCR_015953 | SC3 package, Single-Cell Consensus Clustering | 2026-07-28 09:44:05 | 20 | |||||
|
Gubbins Resource Report Resource Website 500+ mentions |
Gubbins (RRID:SCR_016131) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | rapid, phylogenetic, analysis, large, sample, recombinant, bacteria, whole, genome, sequence, loci, elevated, densities, base, substitiution, mutatiion, outside, region, evolution, alignment |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 098051 | PMID:25414349 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_14386 | https://sources.debian.org/src/gubbins/ | SCR_016131 | Gubbins: Genealogies Unbiased By recomBinations In Nucleotide Sequences | 2026-07-28 09:44:14 | 602 | |||||
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Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | data or information resource, standard specification, narrative resource, portal | Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. | Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list |
is used by: OpenNeuro is used by: SPARC Portal is used by: SPARC Data Standard is listed by: FAIRsharing is related to: BIDS-Matlab is related to: NiPoppy works with: MNE-BIDS |
International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; NIGMS P20 GM103472; Wellcome Trust ; NIAAA U01 AA021697; NIMH Intramural Research Program ; German federal state of Sachsen-Anhalt ; European Regional Development Fund ; Medical Research Council United Kingdom ; NSF 1429999 |
PMID:27326542 PMID:29917016 PMID:31239435 PMID:31239438 PMID:37744469 |
Free, Freely available | https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t | SCR_016124 | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-07-28 09:44:09 | 212 | |||||
|
Stimfit Resource Report Resource Website 10+ mentions |
Stimfit (RRID:SCR_016050) | software application, software resource, data analysis software, data processing software | Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. | electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis |
uses: NumPy uses: SciPy |
European Research Council ; Wellcome Trust ; Gatsby Charitable Foundation |
PMID:24600389 | Free, Available for download | SCR_016050 | 2026-07-28 09:44:03 | 38 | ||||||||
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Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ | SCR_016060 | ClonalFrameML | 2026-07-28 09:44:04 | 379 | |||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | software application, data analysis software, sequence analysis software, software resource, data processing software, data analytics software | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 355804783; Wellcome Trust WT092340; Wellcome Trust WT083481; Wellcome Trust 106370Z14 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2026-07-28 09:44:19 | 126 | ||||||||
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ChEMBL Resource Report Resource Website 1000+ mentions |
ChEMBL (RRID:SCR_014042) | data or information resource, database | Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database. | database, compound, data, bioassay, bioactive, molecule, drug, discovery |
is used by: GEROprotectors is used by: PubChem is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Wellcome Trust ; EMBL Member States ; Medicines for Malaria Ventures ; EU Innovative Medicines Initiative ; GSK ; Syngenta ; Pfizer |
PMID:21948594 | Public, Free, Freely available, Acknowledgement requested | r3d100010539 | https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320 | SCR_014042 | ChEMBLdb, Chembl, ChEMBL Database | 2026-07-28 09:43:41 | 2433 | |||||
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Open Source Brain Resource Report Resource Website 10+ mentions |
Open Source Brain (RRID:SCR_001393) | OSB | service resource, data or information resource, data repository, database, storage service resource | A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome. | model, neuroml, pynn, computational model, neural system, neuron, disease, data analysis service, visualization, 3d explorer, network, ion channel distribution, ion channel, microcircuit |
uses: PyNN uses: NeuroML is used by: NIF Data Federation is listed by: Integrated Models is related to: neuroConstruct is related to: NWB Explorer is related to: Allen Institute for Brain Science has parent organization: University College London; London; United Kingdom |
Wellcome Trust | Free, Freely Available | nlx_152590 | SCR_001393 | OpenSourceBrain | 2026-07-28 09:40:15 | 26 | ||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | software application, data analysis software, software resource, data processing software, data visualization software | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-07-28 09:44:26 | 21 | ||||||||
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SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software application, software resource, data analysis software, data processing software | 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 ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-07-28 09:44:51 | 2 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | software application, software resource, data analysis software, data processing software | 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 ; Wellcome Trust ; Royal Society ; European Research Council |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-07-28 09:44:42 | 1 | ||||||||
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genomics resource for animal lectins Resource Report Resource Website 1+ mentions |
genomics resource for animal lectins (RRID:SCR_018122) | data or information resource, topical portal, portal | Resource presents information about animal lectins involved in various sugar recognition processes. | Genomic, animal lectin, sugar recognition process | has parent organization: Imperial College London; London; United Kingdom | BBSRC ; Wellcome Trust ; Consortium for Functional Glycomics |
Free, Freely available | SCR_018122 | 2026-07-28 09:44:41 | 3 | |||||||||
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EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data or information resource, database, data access protocol, software resource, web service | 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 | 2026-07-28 09:44:53 | 233 | |||||||
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xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | software application, data access protocol, software resource, data processing software, data visualization software, web service | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | Crosslink Network Maps With Residue Resolution | 2026-07-28 09:45:09 | 19 | |||||||
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T1DBase Resource Report Resource Website 100+ mentions |
T1DBase (RRID:SCR_007959) | service resource, resource, data or information resource, data repository, database, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data. | genetics, beta cell, gene, variant, region, genomics, gene expression, genome-wide association study, data analysis service, bio.tools |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is listed by: NIDDK Information Network (dkNET) is listed by: Debian is listed by: bio.tools is related to: dkCOIN has parent organization: University of Cambridge; Cambridge; United Kingdom |
Type 1 diabetes. Diabetes | Wellcome Trust ; NIDDK ; Juvenile Diabetes Research Foundation |
PMID:20937630 | THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-03531, biotools:t1dbase | https://bio.tools/t1dbase | SCR_007959 | T1DBase - Type 1 Diabetes Database | 2026-07-28 09:41:57 | 145 | ||||
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Rfam Resource Report Resource Website 1000+ mentions |
Rfam (RRID:SCR_007891) | Rfam, RFAM | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome | family, genome, clan, structure, non-coding rna, FASEB list | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | Howard Hughes Medical Institute ; University of Manchester; Manchester; United Kingdom ; Wellcome Trust WT077044/Z/05/Z |
PMID:21062808 | http://rfam.sanger.ac.uk/ | SCR_007891 | RFAM, Rfam database | 2026-07-28 09:41:58 | 3693 | ||||||
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ezBIDS Resource Report Resource Website |
ezBIDS (RRID:SCR_025563) | web application, software resource | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | NINDS UM1NS132207; BRAIN CONNECTS ; NIBIB R01EB029272; NIBIB R01EB030896; NSF ; Kavli Foundation ; Wellcome Trust ; NIMH R01MH133701; Spanish Government |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/, | SCR_025563 | ez Brain Imaging Data Structure | 2026-07-27 09:37:26 | 0 | |||||||
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GeneDB Resource Report Resource Website 100+ mentions |
GeneDB (RRID:SCR_002774) | GDB, GeneDB | data set, training resource, data or information resource, database, workshop | Database of genomes at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. Its primary goals are: 1) to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group, and 2) to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. | schizosaccharomyces, pombe, leishmania, major, trypanosoma, brucei, functional, genomics, proteomics, apicomplexan, protozoa, kinetoplastid, parasitic, helminths, bacteria, parasite vector, virus, FASEB list |
is related to: TriTrypDB is related to: Integrated Manually Extracted Annotation has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: GeneDB Gmorsitans is parent organization of: GeneDB Lmajor is parent organization of: GeneDB Tbrucei is parent organization of: GeneDB Pfalciparum is parent organization of: GeneDB Spombe |
Wellcome Trust | PMID:14681429 | Free | nif-0000-02880, r3d100010626 | https://doi.org/10.17616/R31C8X | http://old.genedb.org/, http://www.gdb.org/ | SCR_002774 | GDB, Gene DB | 2026-07-28 09:40:40 | 429 |
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