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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CandiMeth Resource Report Resource Website 1+ mentions |
CandiMeth (RRID:SCR_017974) | CandiMeth | software application, production service resource, data processing software, data analysis software, analysis 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 | 2026-02-17 10:03:41 | 2 | |||||
|
ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, software application, data processing software, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-02-17 10:03:01 | 47 | ||||||
|
VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | data analysis software, software application, data processing 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 | 2026-02-17 10:03:42 | 1 | |||||
|
Warp Resource Report Resource Website 1+ mentions |
Warp (RRID:SCR_018071) | software application, data processing software, data analysis software, 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 | 2026-02-17 10:03:23 | 7 | |||||||
|
RaptorX Resource Report Resource Website 100+ mentions |
RaptorX (RRID:SCR_018118) | data access protocol, software application, software resource, 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 | 2026-02-17 10:03:01 | 149 | ||||||
|
CLIP-Explorer Resource Report Resource Website 1+ mentions |
CLIP-Explorer (RRID:SCR_018128) | software application, data processing software, data analysis software, software resource, service resource, data visualization 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 | 2026-02-17 10:03:44 | 2 | ||||||||
|
PlotTwist Resource Report Resource Website 10+ mentions |
PlotTwist (RRID:SCR_018331) | data access protocol, production service resource, analysis 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 | 2026-02-17 10:03:27 | 10 | ||||||
|
CRISPRcasIdentifier Resource Report Resource Website 1+ mentions |
CRISPRcasIdentifier (RRID:SCR_018296) | data analysis software, software application, data processing software, 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 | 2026-02-17 10:03:44 | 4 | |||||||
|
SpoTyping Resource Report Resource Website 10+ mentions |
SpoTyping (RRID:SCR_018466) | data analysis software, software application, data processing software, 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 | 2026-02-17 10:03:05 | 10 | |||||
|
DAMBE Resource Report Resource Website 1+ mentions |
DAMBE (RRID:SCR_018528) | software application, data processing software, data analysis software, software resource, sequence analysis software | 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 |
Natural Science and Engineering Research Council of Canada ; University of Hong Kong ; Hong Kong Research Grant Council |
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 | 2026-02-17 10:03:46 | 7 | |||||
|
SymPy Resource Report Resource Website 1+ 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 | 2026-02-17 10:03:48 | 9 | ||||||||
|
smashpp Resource Report Resource Website 1+ mentions |
smashpp (RRID:SCR_018307) | software application, data processing software, data analysis software, software resource, data visualization software | 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++ | 2026-02-17 10:03:46 | 2 | |||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | data access protocol, application programming interface, 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 | 2026-02-17 10:03:05 | 2 | |||||||
|
GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | data access protocol, data or information resource, service resource, software resource, web service, portal | 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 | 2026-02-17 10:03:46 | 2 | |||||
|
Graph2GO Resource Report Resource Website 1+ mentions |
Graph2GO (RRID:SCR_018726) | data analysis software, software application, data processing software, 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 | 2026-02-17 10:03:50 | 2 | ||||||||
|
rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-02-17 10:03:07 | 30 | ||||||
|
TRACESPipe Resource Report Resource Website 1+ mentions |
TRACESPipe (RRID:SCR_018831) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data. | Hybrid pipeline, genome reconstruction, genome analysis, viral genome, host genome, multi organ sequencing, multi organ level, DNA sequence data, multiple organ data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.5524/100771 | Free, Freely available | biotools:tracespipe | http://dx.doi.org/10.5524/100771 https://bio.tools/tracespipe |
SCR_018831 | 2026-02-17 10:03:33 | 1 | |||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | software application, data processing software, software resource, image analysis software, alignment software | 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 | 2026-02-17 10:03:49 | 1325 | ||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data visualization software, data processing 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 | 2026-02-17 10:03:47 | 54 | ||||||
|
Robetta Resource Report Resource Website 100+ mentions |
Robetta (RRID:SCR_018805) | data access protocol, production service resource, analysis service resource, service resource, software resource, web service | Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure. | Protein structure prediction, protein, structure prediction, prediction service, automated prediction, analysis tools, genomic data, protein sequence, protein model, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:15215442 | Restricted | biotools:robetta | https://bio.tools/robetta | SCR_018805 | 2026-02-17 10:03:51 | 330 |
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