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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | data visualization software, data analysis software, software application, software resource, data processing software | Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. | Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: University of California at Berkeley; Berkeley; USA |
National Institutes of Health NRSA Trainee appointment ; California Research Alliance by BASF ; NIMH U01 MH105979; NHGRI U01 HG007910 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | 2026-08-01 12:06:05 | 0 | ||||||
|
Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | software resource, data access protocol, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-08-01 12:06:07 | 4 | ||||||
|
Telescope Resource Report Resource Website 1+ mentions |
Telescope (RRID:SCR_017626) | software resource, web application | Open source web application that tracks progress of jobs submitted to remote servers using Sun Grid Engine (SGE) on-demand scheduling system. Allows remote scheduling of pre-defined pipelines, as well as re-scheduling queued jobs. Telescope does not assume anything from the remote server, except for SSH connection. The connection is established using SSH key pairs that are stored after encrypted. | Track, progress, remote, server, scheduling, system, on demand, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Los Angeles; California; USA |
Free, Freely available | biotools:telescope | https://bio.tools/Telescope | SCR_017626 | 2026-08-01 12:06:16 | 2 | ||||||||
|
YASARA Resource Report Resource Website 100+ mentions |
YASARA (RRID:SCR_017591) | YASARA | data visualization software, 3d visualization software, software application, data processing software, software resource, simulation software | Software tool to obtain structural guidance in biocatalytic investigations. Program for molecular visualising, modelling, and dynamics. Initial stage YASARA View is for free while higher stages YASARA Model, YASARA Dynamics, YASARA Structure require license fee. Program for Windows, Linux, MacOS and Android. YASARA View is available for free and contains all functions to explore macromolecular structure interactively. | Biocatalytic, molecular, visualization, modelling, dynamics, macromolecular, structure, interactively, bio.tools |
uses: PDB-REDO is used by: PDB-REDO is listed by: bio.tools is listed by: Debian |
Restricted | biotools:yasara | https://bio.tools/yasara | SCR_017591 | Yasara, Yet Another Scientific Artificial Reality Application | 2026-08-01 12:06:08 | 165 | ||||||
|
AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | data or information resource, database, service resource, production service resource, analysis service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
NIDA ; Department of Health and Human Services ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-08-01 12:06:15 | 7 | ||||||
|
ShinyLearner Resource Report Resource Website 1+ mentions |
ShinyLearner (RRID:SCR_017608) | data processing software, data analysis software, software application, software resource | 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 | 2026-08-01 12:06:08 | 2 | |||||||
|
Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | data or information resource, data repository, storage service resource, database, service resource | Open access database for all cognitive data collected from touchscreen related tasks. Performs data comparison and interactive data visualization for any data uploaded onto the site. There are also guidelines and video tutorials available. | Data, mouse, cognition, imaging, genomics, integration, bio.tools, OpenBehavior |
is listed by: Debian is listed by: bio.tools is listed by: OpenBehavior has parent organization: Western University; Ontario; Canada |
Weston Brain Institute (Canada) ; Canadian Institute of Health Research ; NSERC ; Alzheimer’s Society of Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Brain Canada |
PMID:31825307 | Free, Freely available | SCR_021549, SCR_021598, r3d100013886, biotools:Mousebytes | https://bio.tools/MouseBytes, https://edspace.american.edu/openbehavior/project/touchscreen-cognition-mousebytes/, https://doi.org/10.17616/R31NJN7I | SCR_017904 | MouseBytes | 2026-08-01 12:06:08 | 4 | |||||
|
Mesquite Resource Report Resource Website 100+ mentions |
Mesquite (RRID:SCR_017994) | data processing software, data analysis software, software application, software resource | Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed. | Modular, evolutionary, analysis, organize, comparative data, organism, phylogenetic, population genetic, non-pylogenetic | is listed by: Debian | NSF DEB 1258220; David and Lucile Packard Foundation ; NSERC Discovery grant ; NSF |
Free, Available for download, Freely available | https://sources.debian.org/src/mesquite/ | SCR_017994 | Mesquite 3.04, Mesquite 3.61 | 2026-08-01 12:06:09 | 151 | |||||||
|
4See Resource Report Resource Website 1+ mentions |
4See (RRID:SCR_018014) | data visualization software, software application, data processing software, software resource | Software tool to visualize 4C data. | Visualize, 4C data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.3389/fgene.2019.01372 | Free, Available for download, Freely available | biotools:4see | https://bio.tools/4see | SCR_018014 | 2026-08-01 12:06:17 | 1 | |||||||
|
NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software toolkit, data analysis software, software application, software resource, 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 | 2026-08-01 12:06:09 | 2 | |||||
|
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 | data visualization software, software application, data processing software, software resource | 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 | 2026-08-01 12:06:09 | 4 | ||||
|
BioNix Resource Report Resource Website 1+ mentions |
BioNix (RRID:SCR_017662) | software resource, software library, 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 | 2026-08-01 12:06:16 | 4 | ||||||||
|
PEMA Resource Report Resource Website 1+ mentions |
PEMA (RRID:SCR_017676) | software toolkit, data analysis software, software application, software resource, 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 | 2026-08-01 12:06:08 | 1 | ||||||
|
Anndata Resource Report Resource Website 10+ mentions |
Anndata (RRID:SCR_018209) | software resource, software application, data management software | 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 | 2026-08-01 12:06:18 | 28 | |||||||
|
iTOL Resource Report Resource Website 1000+ mentions |
iTOL (RRID:SCR_018174) | software resource, data access protocol, service resource, web service | 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 | 2026-08-01 12:06:11 | 3161 | |||||
|
MUMmer Resource Report Resource Website 100+ mentions |
MUMmer (RRID:SCR_018171) | image analysis software, alignment software, software application, software resource, 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 | 2026-08-01 12:06:18 | 480 | |||||
|
biospytial Resource Report Resource Website 1+ mentions |
biospytial (RRID:SCR_018226) | data visualization software, software toolkit, data analysis software, data management software, software application, data processing software, software resource | 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 | 2026-08-01 12:05:56 | 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 | 2026-08-01 12:06:18 | 138 | |||||
|
Laniakea Resource Report Resource Website 1+ mentions |
Laniakea (RRID:SCR_018146) | software resource | Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine. | Automatic deployment, virtual Galaxy, life science environment, virtual machine, cloud architecture, Elixir Italy, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ELIXIR Tools and Data Services Registry |
Restricted | biotools:Laniakea | https://bio.tools/Laniakea | SCR_018146 | Galaxy cloud on demand workflow workbench | 2026-08-01 12:06:11 | 1 | |||||||
|
ΔG prediction server Resource Report Resource Website 10+ mentions |
ΔG prediction server (RRID:SCR_018191) | software resource, data access protocol, service resource, web service | 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 | 2026-08-01 12:06:18 | 12 |
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