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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TCGAbiolinks Resource Report Resource Website 100+ mentions |
TCGAbiolinks (RRID:SCR_017683) | data analysis software, data processing software, software resource, software application | Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R. | Integrative, analysis, TCGA data, cancer, genome, atlas, genomic, analysis, expression, methylated, region, survival plot, phenotype, tumor, epigenomic, alteration, clinical, molecular, retrival | BridgeIRIS ; INNOVIRIS ; Region de Bruxelles Capitale ; Brussels ; Belgium ; GENGISCAN ; São Paulo Research Foundation |
PMID:26704973 DOI:10.12688/f1000research.8923.2 |
Free, Available for download, Freely available | https://github.com/BioinformaticsFMRP/TCGAbiolinks | SCR_017683 | Cancer Genome Atlas (TCGA) biolinks | 2026-08-13 09:30:05 | 112 | |||||||
|
Adobe Photoshop Lightroom Resource Report Resource Website 1+ mentions |
Adobe Photoshop Lightroom (RRID:SCR_018012) | image processing software, data processing software, software resource, software application | Camera raw data processing software. Cloud-based service to edit, organize, store, and share photos across any device. | Data, processing, editing, organizing, storing, sharing, photograph, image | is related to: Adobe Photoshop | Restricted | SCR_018012 | 2026-08-13 09:30:15 | 3 | ||||||||||
|
ISB Cancer Genomics Cloud Resource Report Resource Website 10+ mentions |
ISB Cancer Genomics Cloud (RRID:SCR_017681) | ISB-CGC | web application, service resource, data repository, storage service resource, software resource | Web tool as flexible cloud-based platform for cancer genomics research. Platform that serves as large-scale repository and provides computational infrastructure necessary to carry out cancer genomics research at unprecedented scales. ISB-CGC is providing access to TCGA data and computation on Google Cloud Platform. | Cancer, genomics, repository, data | National Cancer Institute ; National Institutes of Health |
PMID:29092928 | Restricted | SCR_017681 | ISB Cancer Genomics Cloud, Institute for Systems Biology Cancer Genomics Cloud | 2026-08-13 09:30:05 | 11 | |||||||
|
GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, data processing software, software resource, software application | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-08-13 09:30:05 | 3 | |||||
|
VariantDB Resource Report Resource Website 1+ mentions |
VariantDB (RRID:SCR_018010) | data or information resource, analysis service resource, production service resource, service resource, portal | Web based interactive annotation and filtering platform that automatically annotates variants with allele frequencies, functional impact, pathogenicity predictions and pathway information. Allows filtering by all annotations, under dominant, recessive or de novo inheritance models. Flexible annotation and filtering portal for next generation sequencing data. | Annotation, filtering, portal, next generation, sequencing data, variant, allele frequency, functional impact, pathogenicity prediction, pathway information | Belgian National Fund for Scientific Research-Flanders ; Fondation Leducq |
PMID:25352915 | Restricted | http://www.biomina.be/app/variantdb/ | SCR_018010 | 2026-08-13 09:30:09 | 1 | ||||||||
|
swMath Resource Report Resource Website 1+ mentions |
swMath (RRID:SCR_017607) | data or information resource, database, software resource, software repository | Repository of math software. Information service for mathematical software. Provides access to database of information on mathematical software and includes systematic linking of software packages with relevant mathematical publications. Database for references on mathematical software. | Repository, math, infromation, service, publication, database | Leibniz Association | Free, Freely available | r3d100014573 | https://doi.org/10.17616/R31NJNQL | SCR_017607 | 2026-08-13 09:30:04 | 2 | ||||||||
|
GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | data or information resource, analysis service resource, production service resource, database, service resource, data analysis service, atlas | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-08-13 09:30:03 | 158 | |||||||||
|
SciGraph Resource Report Resource Website 1+ mentions |
SciGraph (RRID:SCR_017576) | data processing software, software application, data visualization software, standalone software, software resource | Software tool to represent ontologies and data described using ontologies as Neo4j graph. Ontology serving middleware tool using Neo4J as base server, able to ingest ttl files, and serve them to quickly create services that can underpin autocomplete, term lookup and tree traversal. | Ontology, data, Neo4j graph, server, ttl, file |
is used by: SPARC Portal is used by: SciCrunch is used by: CINERGI is used by: Human Brain Project |
Free, Available for download, Freely available | SCR_017576 | 2026-08-13 09:30:04 | 3 | ||||||||||
|
Fusion software Resource Report Resource Website 1+ mentions |
Fusion software (RRID:SCR_017972) | data analysis software, data processing software, software resource, software application | Software for analyzing mouse behavior by Omnitech Electronics Inc. | Analyzing, mouse, behavior, Omnitech Electronics Inc. | SCR_017972 | 2026-08-13 09:30:09 | 4 | ||||||||||||
|
mysamplesize Resource Report Resource Website 1+ mentions |
mysamplesize (RRID:SCR_017575) | data or information resource, data processing software, data analysis software, software application, data visualization software, service resource, software resource, portal | Software tool for experimental design, sample size determination and analysis by Tempest Technologies. | Experimental, design, sample, size, determination, analysis, Tempest Technologies |
is affiliated with: University of California at San Diego; California; USA is affiliated with: University of California at Davis; California; USA |
Restricted | SCR_017575 | MySampleSize | 2026-08-13 09:29:45 | 1 | |||||||||
|
refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | data management software, software resource, service resource, software application | Software tool to organize, retrieve, and share genome analysis resources. Reference genome assembly asset manager. In addition to genome indexes, can manage any files related to reference genomes, including sequences and annotation files. Includes command line interface and server application that provides RESTful API, so it is useful for both tool development and analysis. | Organize, retrive, share, genome, analysis, reference, assembly, asset, manager, sequence, annotation, file, command, line, interface, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/698704 | Free, Available for download, Freely available | biotools:Refgenie | https://bio.tools/Refgenie | SCR_017574 | reference genome manager | 2026-08-13 09:30:04 | 7 | ||||||
|
CRISPy-web Resource Report Resource Website 10+ mentions |
CRISPy-web (RRID:SCR_017970) | data access protocol, software resource, web service | Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction. | Design, sgRNA, CRISP, microbial, genome, Cas9, target, prediction, data, guide, single, editing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Novo Nordisk Foundation | PMID:29062934 | Free, Freely available | biotools:crispy | https://bio.tools/crispy | SCR_017970 | single guide RNA desing | 2026-08-13 09:30:15 | 28 | |||||
|
PoloPlus USB Drive software Resource Report Resource Website 10+ mentions |
PoloPlus USB Drive software (RRID:SCR_017614) | data analysis software, data processing software, software resource, software application | Software to perform Probit and Logit analsis with grouped data. Original Polo Software available through USB Drive. Able to work on all versions of Windows as all files are kept on USB. | LeOra Software LLC, grouped, data, analysis, USB, drive, probit, logit | Restricted | SCR_017614 | Probit Or LOgit Plus USB Drive, PoloPlus USB Drive | 2026-08-13 09:30:04 | 35 | ||||||||||
|
PAFScaff Resource Report Resource Website 1+ mentions |
PAFScaff (RRID:SCR_017976) | data analysis software, data processing software, software application, software resource, sequence analysis software | Software as Pairwise mApping Format reference based Scaffold anchoring and super scaffolding tool. Dsigned for mapping genome assembly scaffolds to closely related chromosome level reference genome assembly. | Pairwise, mapping, reference, scaffold, genomics, scaffolding, assembly, genome, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:PAFScaff | https://github.com/slimsuite/pafscaff/blob/master/PAFScaff.md, https://slimsuite.github.io/pafscaff/, https://bio.tools/PAFScaff | SCR_017976 | Pairwise mApping Format reference-based Scaffold | 2026-08-13 09:29:56 | 4 | |||||||
|
EBRAINS Knowledge Graph Resource Report Resource Website 1+ mentions |
EBRAINS Knowledge Graph (RRID:SCR_017612) | data or information resource, data management software, software application, database, service resource, software resource | Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems. | Metadata, managing, system, neuroscience, experimental, data, human, brain, graph, database, terminology, ontology |
is related to: Human Brain Project is related to: MarmotGraph |
European Union’s Horizon 2020 Framework Programme for Research and Innovation 720270; European Union’s Horizon 2020 Framework Programme for Research and Innovation 785907 |
Free, Freely available | https://kg.humanbrainproject.eu/ | SCR_017612 | New Enabling Infrastructure for Neuroscience Knowledge Graph, EBRAINS Knowledge Graph (KG), HBP Knowledge Graph | 2026-08-13 09:29:46 | 8 | |||||||
|
CandiMeth Resource Report Resource Website 1+ mentions |
CandiMeth (RRID:SCR_017974) | CandiMeth | data analysis software, data processing software, software application, analysis service resource, production service resource, service resource, software resource | Software tool for visualisation and quantification of DNA methylation at candidate features. | DNA, methylation, candidate feature, visualisation, quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy |
Medical Research Council ; ESRC/BBSRC |
Free, Freely available | biotools:CandiMeth | http://bit.do/candimeth, https://usegalaxy.org/u/sarajayne-thursby/w/candimeth-8, https://bio.tools/CandiMeth | SCR_017974 | CANDIdate feature METHylation | 2026-08-13 09:30:15 | 2 | |||||
|
rjags Resource Report Resource Website 10+ mentions |
rjags (RRID:SCR_017573) | data analysis software, data processing software, software resource, software application | Software package provides interface from R to JAGS library for Bayesian data analysis. Program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. | Analysis, Bayesian, hierarchical, model, Markov Chain Monte Carlo, simulation |
is listed by: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | https://github.com/cran/rjags/blob/master/INSTALL | SCR_017573 | RJAGS library | 2026-08-13 09:30:03 | 23 | ||||||||
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VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | data analysis software, data processing software, software resource, software application | Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases. | FANTOM5 consortium, data, CAGE enhancer, transcription site database, intersectional genetics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/552984 | Free, Available for download, Freely available | BioTools:VEnCode, biotools:VEnCode | https://bio.tools/VEnCode, https://bio.tools/VEnCode, https://bio.tools/VEnCode | SCR_018024 | Versatile Entry Codes | 2026-08-13 09:30:09 | 1 | |||||
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Warp Resource Report Resource Website 10+ mentions |
Warp (RRID:SCR_018071) | data analysis software, data processing software, software application, data acquisition software, software resource | Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising. | Automating preprocessing step, cryo EM data acquisition, micrograph correction, particle picking, image denoising, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1038/s41592-019-0580-y | Free, Available for download, Freely available | BioTools:Warp, biotools:Warp | https://bio.tools/Warp, https://bio.tools/Warp, https://bio.tools/Warp | SCR_018071 | 2026-08-13 09:29:57 | 10 | |||||||
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Worm Lab Resource Report Resource Website 1+ mentions |
Worm Lab (RRID:SCR_017669) | data analysis software, data processing software, software resource, software application | Software tool for imaging, tracking, and analyzing C. elegans and other nematodes. It has user friendly software interface with patented model specific tracking algorithm that collects data about single worm or multiple worms, even through omega bends, coiling, reversals, and entanglements. Provides quantitative analysis of locomotory behavior with user configurable metrics for crawling and swimming assays. | MBF Bioscience, imaging, tracking, analysis, C.elegans, nematode, collect, data, worm, omega, bend, coiling, reversal, entanglement, locomotry, behavior, crawling, swimming, assay | Restricted | SCR_017669 | 2026-08-13 09:29:47 | 8 |
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