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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
mirTools Resource Report Resource Website 10+ mentions |
mirTools (RRID:SCR_009701) | mirTools | analysis service resource, data analysis service, production service resource, service resource | A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23778453 | OMICS_00365, biotools:mirtools | https://bio.tools/mirtools | SCR_009701 | mirTools 2.0 | 2026-08-07 09:27:07 | 13 | ||||||
|
ShinyLearner Resource Report Resource Website 1+ mentions |
ShinyLearner (RRID:SCR_017608) | software resource, software application, data analysis software, data processing software | Software framework for performing benchmarks of machine learning classification algorithms. Containerized benchmarking tool for machine-learning classification of tabular data. | Benchmark, machine, learning, classification, algorithm, tabular, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/675181 | Free, Available for download, Freely available | biotools:ShinyLearner | https://bio.tools/ShinyLearner | SCR_017608 | 2026-08-07 09:28:59 | 2 | |||||||
|
NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software toolkit, software resource, software application, data analysis software, data processing software | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-08-07 09:28:56 | 2 | |||||
|
BioNix Resource Report Resource Website 1+ mentions |
BioNix (RRID:SCR_017662) | software library, software resource, software toolkit | Software tool for reproducible bioinformatics that unifies workflow engines, package managers, and containers. Implemented as lightweight library on top of Nix deployment system. Bioinformatics workflows in functional Nix language. | Workflow, engine, package, manager, container, unify, bioinformatics, Nix, functional, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:bioNix | https://bio.tools/BioNix | SCR_017662 | 2026-08-07 09:28:49 | 4 | ||||||||
|
PEMA Resource Report Resource Website 1+ mentions |
PEMA (RRID:SCR_017676) | software toolkit, software resource, software application, data analysis software, data processing software | Software as flexible pipeline for environmental DNA metabarcoding analysis of 16S/18S rRNA, ITS and COI marker genes. Performs reads’ pre-processing, clustering to (M)OTUs and taxonomy assignment for 16S rRNA and COI marker gene data. Allows users to explore alternative algorithms for specific steps of pipeline without need of complete re-execution. | Environmental, DNA, metabarcoding, analysis, ASVs, OTUs, 16S rRNA, COI, ITS, marker, gene, clustering, taxonomy, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/709113 | Free, Freely available | biotools:PEMA | https://docs.google.com/presentation/d/1lVH23DPa2NDNBhVvOTRoip8mraw8zfw8VQwbK4vkB1U/edit?fbclid=IwAR14PpWfPtxB8lLBBnoxs7UbG3IJfkArrJBS5f2kRA__kvGDUb8wiJ2Cy_s#slide=id.g57f092f54d_1_21, https://bio.tools/PEMA | SCR_017676 | Pipeline for Environmental DNA Metabarcoding Analysis | 2026-08-07 09:29:00 | 1 | ||||||
|
Anndata Resource Report Resource Website 10+ mentions |
Anndata (RRID:SCR_018209) | data management software, software resource, software application | Software tool that provides scalable way of keeping track of data and learned annotations. Initially built for Scanpy. Used as generic class for handling annotated data matrices. Stores data matrix with annotations of observations (samples, cells) and variables (features, genes), and unstructured annotations. | Data tracking, annotated data matrice, store data matrix, annotation of observation, annotation of variable, unstructured annotation, sparse data, |
is listed by: Debian is related to: scanpy |
Helmholtz Postdoc Programme ; German Research Foundation |
PMID:29409532 | https://sources.debian.org/src/python3-anndata/ | SCR_018209 | Annotated data | 2026-08-07 09:29:06 | 33 | |||||||
|
iTOL Resource Report Resource Website 5000+ mentions |
iTOL (RRID:SCR_018174) | software resource, data access protocol, web service, service resource | Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser. | Phylogenetic tree, phylogeny, data visualization, data annotation, data management, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Federal Ministry of Education and Research ; European Research Council ; European Molecular Biology Laboratory |
PMID:30931475 | Free, Freely available | biotools:itol | https://bio.tools/itol | SCR_018174 | interactive Tree Of Life | 2026-08-07 09:28:58 | 5217 | |||||
|
MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | image analysis software, software resource, software application, alignment software, data processing software | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-08-07 09:28:58 | 547 | |||||
|
biospytial Resource Report Resource Website 1+ mentions |
biospytial (RRID:SCR_018226) | software toolkit, software resource, software application, data management software, data analysis software, data visualization software, data processing software | Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system. | spatial data infrastructure, biodiversity informatics, ecological knowledge engine, ecological data analysis, biodiversity, taxonomic classification, bio.tools |
is listed by: Debian is listed by: bio.tools |
CONACyT ; GBIF ; Lancaster University |
DOI:10.5524/100723 | Free, Available for download, Freely available | biotools:biospytial | https://bio.tools/biospytial | SCR_018226 | 2026-08-07 09:28:57 | 2 | ||||||
|
NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | software resource, data access protocol, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-08-07 09:28:59 | 169 | |||||
|
TDimpute Resource Report Resource Website 1+ mentions |
TDimpute (RRID:SCR_018306) | software resource, software application, data analysis software, data processing software | Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data. | Transfer learning; gene expression prediction; DNA methylation; TCGA, neural network, missing gene expression, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/803692 | Free, Available for download, Freely available | biotools:tDimpute, BioTools:TDimpute | https://bio.tools/TDimpute, https://bio.tools/TDimpute, https://bio.tools/TDimpute | SCR_018306 | 2026-08-07 09:29:01 | 1 | |||||||
|
Online Peri-Event Time Histogram for Open Ephys Resource Report Resource Website 1+ mentions |
Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) | OPETH | software resource, software application, data visualization software, data processing software | Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them. | Open source, open ephys, optogenetics, behavior, electrophysiology data, neuroscience experiment, spike detection, behavior tagging, neuron, histogram, bio.tools |
is listed by: Debian is listed by: bio.tools |
Hungarian Academy of Sciences Lendület Program LP2015-2/2015; European Research Council Starting Grant 715043; Generalitat Valenciana Postdoctoral Fellowship Program APOSTD/2019/003 |
DOI:10.1101/783688 | Free, Available for download, Freely available | biotools:OPEtH | https://bio.tools/OPETH | SCR_018022 | Online Peri-Event Time Histogram | 2026-08-07 09:29:04 | 4 | ||||
|
ΔG prediction server Resource Report Resource Website 10+ mentions |
ΔG prediction server (RRID:SCR_018191) | software resource, data access protocol, web service, service resource | Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon. | Amino acid sequence, putative transmembrane helix, free energy difference, sequence insertion, endoplasmic reticulum membrane, potential TM helix, predict energy difference, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stockholm University; Stockholm; Sweden |
Free, Freely available | biotools:deltag_prediction | http://dgpred.cbr.su.se/index.php?p=TMpred, https://bio.tools/deltag_prediction | SCR_018191 | ΔG prediction server v1.0 | 2026-08-07 09:29:06 | 17 | |||||||
|
Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software resource, software application, data analysis software, data visualization software, data processing software | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org, https://bio.tools/mvp_a | SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-08-07 09:28:55 | 2 | |||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-08-07 09:28:55 | 90 | ||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | sequence analysis software, production service resource, software resource, software application, data analysis software, service resource, analysis service resource, data processing software | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-08-07 09:28:55 | 7206 | |||||
|
Plant Co-expression Annotation Resource Resource Report Resource Website 1+ mentions |
Plant Co-expression Annotation Resource (RRID:SCR_018429) | Plantannot | data or information resource, web service, software resource, data access protocol, service resource | Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard. | Omics, plant, annotation, function, breeding, genetically modified crops, abiotic stress in plant, plant genome, plant genomic data, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Phytozome is related to: NCBI is related to: Machado |
Embrapa | DOI:10.1101/2020.05.22.110510 | Free, Freely available | biotools:plantannot | https://www.machado.cnptia.embrapa.br/plantannot2, https://bio.tools/plantannot | SCR_018429 | Plantannot v2 | 2026-08-07 09:29:00 | 1 | ||||
|
pepwheel Resource Report Resource Website 1+ mentions |
pepwheel (RRID:SCR_018398) | software resource, data access protocol, web service, service resource | Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation. | Computational proteomics, data analysis pipeline, label free quantification, mass spectrometry, quantitative proteomics, visualise protein sequence, helical wheel diagram, peptice sequence display, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: EMBOSS works with: Proteome Discoverer |
Free, Freely available | biotools:pepwheel | https://bio.tools/pepwheel | SCR_018398 | 2026-08-07 09:29:03 | 2 | ||||||||
|
MaxAlign Resource Report Resource Website 10+ mentions |
MaxAlign (RRID:SCR_018552) | production service resource, web service, software resource, data access protocol, data analysis service, analysis service resource, service resource | Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area. | Maximizing data, post process alignment, gap free column alignment area, sequence subset selection, improve alignment area, bio.tools |
is listed by: Debian is listed by: bio.tools |
Foundation for Science and Technology Portuguese Ministry of Science. | PMID:17725821 | Free, Available for download, Freely available | biotools:maxalign | https://bio.tools/maxalign | SCR_018552 | MaxAlign 1.1, MaxAlign 1.1 Server | 2026-08-07 09:29:01 | 11 | |||||
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GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | production service resource, web service, software resource, data access protocol, analysis service resource, service resource | Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. | Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Seoul National University. |
PMID:23737448 | biotools:galaxyrefine | https://bio.tools/galaxyrefine | SCR_018531 | 2026-08-07 09:29:09 | 316 |
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