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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Fcirc Resource Report Resource Website 1+ mentions |
Fcirc (RRID:SCR_018090) | Fcirc | data processing software, software application, software resource, workflow software | 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 Key Research and Development Program 2017YFC0908500 ; National Natural Science Foundation of China 31571363 ; National Natural Science Foundation of China 31771469 ; National Natural Science Foundation of China 81573023 |
Free, Available for download, Freely available | biotools:Fcirc | https://bio.tools/Fcirc | SCR_018090 | Comprehensive Pipeline for Exploration of Fusion Linear and Circular RNAs | 2026-09-05 06:28:31 | 2 | |||||
|
HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | data access protocol, service resource, software resource, web service | 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 | 2026-09-05 06:28:31 | 4 | |||||||
|
Warp Resource Report Resource Website 10+ mentions |
Warp (RRID:SCR_018071) | data acquisition software, data analysis software, data processing software, software application, 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 | 2026-09-05 06:28:30 | 10 | |||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, simulation software, software application, software resource, web service | 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 | 2026-09-05 06:28:31 | 198 | ||||||
|
CLIP-Explorer Resource Report Resource Website 1+ mentions |
CLIP-Explorer (RRID:SCR_018128) | data analysis software, data processing software, data visualization software, service resource, software application, software resource | 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 | 2026-09-05 06:28:31 | 2 | ||||||||
|
NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | simulation software, software application, 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 |
British Columbia Cancer Foundation ; Genome British Columbia ; Genome Canada ; NHGRI R01 HG007182; 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 | 2026-09-05 06:28:33 | 21 | ||||||
|
PlotTwist Resource Report Resource Website 10+ mentions |
PlotTwist (RRID:SCR_018331) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | 2026-09-05 06:28:34 | 12 | ||||||
|
CRISPRcasIdentifier Resource Report Resource Website 1+ mentions |
CRISPRcasIdentifier (RRID:SCR_018296) | data analysis software, data processing software, software application, software resource | Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes. | CRISPR-Cas, Machine Learning, Cas genes, Cas proteins, input protein cassette, predicting subtype, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/817619 | Free, Available for download, Freely available | biotools:crisprcasidentifier | https://bio.tools/crisprcasidentifier | SCR_018296 | 2026-09-05 06:28:34 | 5 | |||||||
|
SymPy Resource Report Resource Website 10+ mentions |
SymPy (RRID:SCR_018417) | software library, software resource, software toolkit | Software Python library for symbolic mathematics. It aims to become full featured computer algebra system (CAS) while keeping code as simple as possible in order to be comprehensible and easily extensible. | Python, Python library, symbolic mathematics, computer algebra system, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:SymPy | https://bio.tools/SymPy | SCR_018417 | 2026-09-05 06:28:36 | 10 | ||||||||
|
smashpp Resource Report Resource Website 1+ mentions |
smashpp (RRID:SCR_018307) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool to find and visualize rearrangements in DNA sequences. | Find sequence rearrangement, visualize sequence rearrangement, DNA, DNA sequence, DNA sequence rearrangement, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:smashpp, BioTools:smashpp | https://bio.tools/smashpp, https://bio.tools/smashpp, https://bio.tools/smashpp | SCR_018307 | Smash++ | 2026-09-05 06:28:34 | 2 | |||||||
|
GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | data access protocol, data or information resource, portal, service resource, software resource, web service | 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 |
Guangdong Natural Science Funds for Distinguished Young Scholar ; International Science and Technology Cooperation Program of China ; National Basic Research Program ; National Natural Science Foundation of China ; Zhujiang Nova Program of Guangzhou |
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 | 2026-09-05 06:28:33 | 6 | |||||
|
SpoTyping Resource Report Resource Website 10+ mentions |
SpoTyping (RRID:SCR_018466) | data analysis software, data processing software, software application, software resource | Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads. | bio.tools |
is listed by: bio.tools is listed by: Debian |
National University of Singapore ; Singapore ; Singapore |
DOI:10.1186/s13073-016-0270-7 | Free, Available for download, Freely available | biotools:spotyping | https://bio.tools/spotyping | SCR_018466 | SpoTyping-v2.0, SpoTyping | 2026-09-05 06:28:37 | 12 | |||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-09-05 06:28:38 | 1593 | ||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data processing software, data visualization software, software application, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-09-05 06:28:38 | 61 | ||||||
|
DAMBE Resource Report Resource Website 10+ mentions |
DAMBE (RRID:SCR_018528) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Hong Kong Research Grant Council ; Natural Science and Engineering Research Council of Canada ; University of Hong Kong |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2026-09-05 06:28:37 | 12 | |||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIAID P30 AI027757; NIAID P30 AI050409; NICHD R01 HD068395; NICHD R21 HD075662; NICHD T32 HD007543; NIDA P30 DA027828; NIMH R21 MH112449 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-09-05 06:28:38 | 8 | ||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | application programming interface, data access protocol, data or information resource, software resource, web service | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-09-05 06:28:36 | 2 | |||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | Protein Structure Analysis web | 2026-09-05 06:28:38 | 109 | |||||
|
Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data analysis software, data processing software, software application, software resource | Software tool as graph based representation learning method for protein function prediction. Multi modal graph based representation learning model that can integrate heterogeneous information including multiple types of interaction networks including sequence similarity network and protein-protein interaction network, and protein features including amino acid sequence, sub cellular location and protein domains, to predict protein functions on Gene Ontology. | Protein function prediction, graph neural network, attributed network embedding, representation learning, multi-modal model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Ohio State University College of Medicine; Ohio; USA |
Free, Available for download, Freely available | SCR_018727, biotools:graph2go | https://integrativeomics.shinyapps.io/graph2go/, https://bio.tools/graph2go | SCR_018726 | 2026-09-05 06:28:41 | 2 | ||||||||
|
BioSimulations Resource Report Resource Website 1+ mentions |
BioSimulations (RRID:SCR_018733) | software resource, web application | Web tool for sharing and re-using biomodels, simulations, and visualizations of simulations results. Supports variety of modeling frameworks including kinetic, constraint based, and logical modeling, model formats including BNGL, CellML, SBML, and simulation tools including COPASI, libRoadRunner/tellurium, NFSim, VCell. | Sharing, reusing, biomodel, simulation, visualization, simulation result, modeling framework support, simulation tool support, model format support, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA has parent organization: University of Connecticut; Connecticut; USA |
NIBIB P41 EB023912; NIGMS ; NSF |
Restricted | biotools:biosimulations | https://bio.tools/biosimulations | SCR_018733 | 2026-09-05 06:28:41 | 1 |
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