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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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fineSTRUCTURE Resource Report Resource Website 10+ mentions |
fineSTRUCTURE (RRID:SCR_018170) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:22:11 | 23 | |||||||
|
ChiCMaxima Resource Report Resource Website 1+ mentions |
ChiCMaxima (RRID:SCR_018178) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | 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 | 2026-02-15 09:22:11 | 2 | |||||||
|
SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | web application, software resource | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2026-02-15 09:22:11 | 1 | |||||||
|
SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software application, data processing software, data analysis software, 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 ; 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 | 2026-02-15 09:22:19 | 2 | ||||||
|
MaxTRAQ Resource Report Resource Website 1+ mentions |
MaxTRAQ (RRID:SCR_018188) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:21:33 | 1 | ||||||||||
|
NeMO Analytics Resource Report Resource Website 10+ mentions |
NeMO Analytics (RRID:SCR_018164) | portal, data analysis service, service resource, production service resource, data or information resource, topical portal, analysis service resource | 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 | 2026-02-15 09:22:11 | 13 | ||||||||
|
Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | workflow software, software application, data processing software, software resource | Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs. | Fusion gene, linear and circular RNA, fusion exploration, RNAseq data, linear transcript, circRNA, gene, data, pipeline, bio.tools |
uses: HISAT2 uses: SAMTOOLS is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 81573023 ; National Key Research and Development Program 2017YFC0908500 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-02-15 09:21:31 | 2 | |||||
|
Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | database, software resource, data access protocol, web service, data or information resource | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. | Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis | has parent organization: La Jolla Institute for Immunology | William K. Bowes Jr Foundation ; NIAID R24 AI108564; NCRR S10 RR027366; NIH Office of the Director S10 OD016262 |
PMID:30449622 | Free, Freely available | SCR_018259 | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics | 2026-02-15 09:22:19 | 59 | ||||||
|
Adobe Photoshop Lightroom Resource Report Resource Website 1+ mentions |
Adobe Photoshop Lightroom (RRID:SCR_018012) | software application, image processing software, data processing software, software resource | 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 | 2026-02-15 09:21:31 | 3 | ||||||||||
|
SonarCloud Vulnerable Code Prospector for C Resource Report Resource Website |
SonarCloud Vulnerable Code Prospector for C (RRID:SCR_018011) | SVCP4C | data set, service resource, storage service resource, data repository, data or information resource | Software tool to collect vulnerable source code from open-source repositories linked to SonarCloud. Dataset repository with tagged files with BufferOverflow features associated to source code repositories publicly available. | Repository, SonarCloud, data, dataset, BufferOverflow | DOI:10.3390/app10041270 | Free, Available for download, Freely available | SCR_018011 | SonarCloud Vulnerable Code Prospector for C, SVCP4CDataset | 2026-02-15 09:22:10 | 0 | ||||||||
|
VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:18 | 1 | |||||
|
gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | software application, data processing software, data analysis software, 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 | 2026-02-15 09:22:19 | 53 | |||||||
|
QIIME 2 View Resource Report Resource Website 50+ mentions |
QIIME 2 View (RRID:SCR_018074) | software application, data visualization software, data processing software, software resource, service resource, data acquisition software | Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided. | QIIME 2, visualization, data, interface, file viewing, file download and displaying | Free, Freely available | https://github.com/qiime2/q2view | SCR_018074 | q2view | 2026-02-15 09:22:10 | 71 | |||||||||
|
PremierBiosoft Proteo IQ Software Resource Report Resource Website 10+ mentions |
PremierBiosoft Proteo IQ Software (RRID:SCR_018072) | software application, data processing software, software resource, data analytics software, data analysis software | Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS. | Proteomic, qualitative, quantitative, protein identification, data, PREMIER Biosoft, mass spectrometry data, database search engine |
works with: GenBank works with: UniProtKB works with: IPI |
Restricted | SCR_018072 | ProteoIQ | 2026-02-15 09:22:10 | 34 | |||||||||
|
CircaDB Resource Report Resource Website 10+ mentions |
CircaDB (RRID:SCR_018078) | CircaDB | database, software resource, data access protocol, web service, data or information resource | Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans. | Mammalian circadian gene, gene expression, expression profile, mice, human, gene annotation, data, time course expression data | PMID:23180795 | Free, Freely available | http://github.com/itmat/circadb | SCR_018078 | Circadian gene expression profiles DataBase | 2026-02-15 09:22:10 | 19 | |||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | software application, data processing software, software resource, software toolkit, data analysis software | 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 | 2026-02-15 09:22:18 | 2 | |||||||||
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Vivli Resource Report Resource Website 1000+ mentions |
Vivli (RRID:SCR_018080) | nonprofit organization, data or information resource, service resource | Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials. | Global data sharing, clinical research data, data, sharing, analytical platform, clinical trial, COVID-19-related trials |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is listed by: Data and Computational Resources to Address COVID-19 is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing |
COVID-19 | Doris Duke Charitable Foundation ; Leona M. and Harry B. Helmsley Charitable Trust ; Lyda Hill Philanthropies ; Phrma |
Restricted | DOI:10.17616/R3SB9S, DOI:10.25504/FAIRsharing.uovQrT, DOI:10.25934, r3d100012823 | https://vivli.org/vivli-covid-19-portal-2/ https://doi.org/10.17616/R3SB9S https://doi.org/10.17616/r3sb9s https://doi.org/10.25934/ https://dx.doi.org/10.25934/ https://fairsharing.org/10.25504/FAIRsharing.uovQrT https://doi.org/10.17616/R3SB9S |
SCR_018080 | 2026-02-15 09:22:18 | 1532 | ||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | software application, data processing software, software resource, software toolkit, data analysis software | 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 | 2026-02-15 09:22:10 | 6 | |||||||||||
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redcap-importer Resource Report Resource Website |
redcap-importer (RRID:SCR_016032) | software application, data processing software, data acquisition software, software resource | Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. | automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import | is related to: University of California at San Diego; California; USA | NIDA U24 DA041123 | Free, Available for download | SCR_016032 | 2026-02-15 09:21:01 | 0 | |||||||||
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Bio-tradis Resource Report Resource Website 50+ mentions |
Bio-tradis (RRID:SCR_015993) | TraDIS:Transposon Directed Insertion Sequencing | software application, sequence analysis software, data processing software, software resource, software toolkit, data analysis software | 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 | 2026-02-15 09:21:00 | 51 |
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