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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | software application, data processing software, data analysis software, software resource | 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 | 2026-02-15 09:22:05 | 3 | |||||
|
shinyGEO Resource Report Resource Website |
shinyGEO (RRID:SCR_017605) | software resource, web application, service resource, production service resource, analysis service resource | Web based tool to download gene expression datasets from GEO in order to perform differential expression and survival analysis for gene of interest. Produces publication ready graphics and generates R code ensuring that all analyses are reproducible. Web based application for analyzing gene expression omnibus datasets. | Gene, expression, dataset, GEO, differencial, analysis, gene, graphic, omnibus, data, bio.tools |
uses: Shiny is listed by: Debian is listed by: bio.tools has parent organization: Eastern Connecticut State University; Connecticut; United States works with: Gene Expression Omnibus (GEO) |
Google Summer of Code | PMID:27503226 | Free, Available for download, Freely available | biotools:shinygeo | https://gdancik.github.io/shinyGEO/ https://bio.tools/shinygeo |
SCR_017605 | 2026-02-15 09:22:04 | 0 | ||||||
|
refgenie Resource Report Resource Website 1+ mentions |
refgenie (RRID:SCR_017574) | data management software, software application, service resource, software resource | 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 | 2026-02-15 09:22:08 | 6 | ||||||
|
CRISPy-web Resource Report Resource Website 10+ mentions |
CRISPy-web (RRID:SCR_017970) | web service, data access protocol, software resource | 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 | 2026-02-15 09:22:09 | 25 | |||||
|
PAFScaff Resource Report Resource Website 1+ mentions |
PAFScaff (RRID:SCR_017976) | software application, sequence analysis software, data processing software, software resource, data 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 | 2026-02-15 09:21:30 | 4 | |||||||
|
CandiMeth Resource Report Resource Website 1+ mentions |
CandiMeth (RRID:SCR_017974) | CandiMeth | software application, data processing software, software resource, service resource, production service resource, analysis service resource, data analysis software | 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 | 2026-02-15 09:22:09 | 2 | |||||
|
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 | ||||||
|
CRISPRdirect Resource Report Resource Website 100+ mentions |
CRISPRdirect (RRID:SCR_018186) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. | CRISP/Cas guide RNA, reduced off target site, design of CRISP/Cas target, selecting rational target, sequence, genomic sequence, RNA, bio.tools |
is listed by: Debian is listed by: bio.tools |
Japan Science and Technology Agency ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:25414360 | Free, Freely available | biotools:CRISPRdirect | https://bio.tools/CRISPRdirect | SCR_018186 | 2026-02-15 09:22:11 | 452 | ||||||
|
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 | |||||
|
HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | web service, data access protocol, service resource, software resource | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | 2026-02-15 09:22:10 | 4 | |||||||
|
GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | portal, software resource, data access protocol, web service, service resource, data or information resource | Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup. | Small ubiquitin like modifier, SUMOs, sumoylation, covalently modified protein, group prediction system, site prediction, interaction motif in protein, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; National Basic Research Program ; Guangdong Natural Science Funds for Distinguished Young Scholar ; Zhujiang Nova Program of Guangzhou ; International Science and Technology Cooperation Program of China |
PMID:24880689 | Restricted | biotools:gps-sumo | http://sumosp.biocuckoo.org/online.php https://bio.tools/gps-sumo |
SCR_018261 | Group-based Prediction System -Small Ubiquitin-like MOdifiers, Small Ubiquitin-like MOdifiers sp, GPS-SUMO 2.0, SUMOsp, GPS Small Ubiquitin-like MOdifiers, Group-based Prediction System-SUMO | 2026-02-15 09:22:12 | 2 | |||||
|
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 | |||||
|
Warp Resource Report Resource Website 1+ mentions |
Warp (RRID:SCR_018071) | software application, data processing software, software resource, data acquisition software, data analysis software | 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 | 2026-02-15 09:22:18 | 7 | |||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | software application, software resource, data access protocol, web service, simulation software | Software package and web server for protein structure and function prediction. Used for predicting 3D structures for protein sequences without close homologs in Protein Data Bank. Given input sequence, predicts its secondary and tertiary structures, contacts, solvent accessibility, disordered regions and binding sites. Assigns some confidence scores to indicate quality of predicted 3D model. | Protein structure predictor, 3D structure, protein sequence, secondary and tertiary structure, binding site, solvent accessibility, disordered region, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Chicago; Illinois; USA |
NIGMS R01 GM089753; NSF DBI 0960390 |
PMID:21987485 | Restricted | biotools:raptorx | https://bio.tools/raptorx | SCR_018118 | 2026-02-15 09:22:10 | 149 | ||||||
|
CLIP-Explorer Resource Report Resource Website 1+ mentions |
CLIP-Explorer (RRID:SCR_018128) | software application, data visualization software, data processing software, software resource, service resource, data analysis software | Webserver to process, analyse and visualise CLIP-Seq data. Software tools to process and visualise RNA protein interactions. CLIP-Seq data analysis in Galaxy. Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP, iCLIP, and with simple changes to iCLIP workflows also FLASH, and uvCLAP. | CLIP-seq data, RNA protein interaction, Galaxy, data analysis, eCLIP, iCLIP, FLASH, uvCLAP, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: FLASH |
Restricted | SCR_018130, biotools:CLIP-Explorer | https://bio.tools/CLIP-Explorer | SCR_018128 | 2026-02-15 09:22:10 | 2 | ||||||||
|
NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | software application, simulation software, software resource | Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. | Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI R01 HG007182; Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; University of British Columbia |
DOI:10.1093/gigascience/gix010 | Free, Available for download, Freely available | biotools:trans-nanosim, biotools:nanosim | https://www.bcgsc.ca/resources/software/nanosim https://bio.tools/nanosim https://bio.tools/Trans-NanoSim |
SCR_018243 | 2026-02-15 09:22:12 | 18 | ||||||
|
PlotTwist Resource Report Resource Website 10+ mentions |
PlotTwist (RRID:SCR_018331) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics. | Plotting continuous data, annotating continuous data, data visualization, time series data, line plot, small multiples, heatmap, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31929523 | Free, Freely available | biotools:Plottwist, BioTools:PlotTwist | https://github.com/JoachimGoedhart/PlotTwist https://bio.tools/PlotTwist https://bio.tools/PlotTwist https://bio.tools/PlotTwist |
SCR_018331 | PlotTwist Shiny | 2026-02-15 09:22:12 | 10 |
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