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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BCBtoolkit Resource Report Resource Website 50+ mentions |
BCBtoolkit (RRID:SCR_015519) | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas. | brain lesion, brain disconnection, white matter, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: NIH Human Connectome Project |
Open source, Free, Available for download, Available on Mac OS, Available on Linux | biotools:bcbtoolkit | https://bio.tools/bcbtoolkit | SCR_015519 | SciCrunch Registry | BCBtoolkit 4.0 | 2026-09-26 02:15:34 | 66 | |||||||
|
MS-GF+ Resource Report Resource Website 100+ mentions |
MS-GF+ (RRID:SCR_015646) | software resource | Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. | protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Pacific Northwest National Laboratory |
NCRR RR018522; NCRR 1-P41-RR024851; NIAID ; W.R. Wiley Environmental Molecular Science Laboratory |
PMID:25358478 | Free, Available for download, Acknowledgment requested | biotools:ms-gf | https://github.com/sangtaekim/msgfplus, https://bio.tools/ms-gf | SCR_015646 | SciCrunch Registry | MSGF+, MSGFPlus | 2026-09-26 02:15:35 | 159 | |||||
|
PanoramaWeb Resource Report Resource Website |
PanoramaWeb (RRID:SCR_017136) | data access protocol, data or information resource, data repository, service resource, software resource, storage service resource, web service | Repository software for targeted mass spectrometry assays from Skyline. Targeted proteomics knowledge base. Public repository for quantitative data sets processed in Skyline. Facilitates viewing, sharing, and disseminating results contained in Skyline documents. | repository, software, targeted, mass, spectrometry, data, proteomic, quantitative, viewing, sharing, disseminating, result, , bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA works with: Skyline |
NHGRI U54 HG008097; NIGMS R01 GM103551; NIGMS R01 GM121696; NIH R01 AR071762; University of Washington Proteomics Resource |
DOI:10.1074/mcp.RA117.000543 | Free, Freely available | biotools:panorama | https://bio.tools/panorama | SCR_017136 | SciCrunch Registry | 2026-09-26 02:15:57 | 0 | ||||||
|
ascend Resource Report Resource Website 1+ mentions |
ascend (RRID:SCR_017257) | data analysis software, data processing software, software application, software resource | Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions. | analysis, single, cell, RNAseq, expression, normalization, data, gene, filtering, quality, control, dimension, reduction, clustering, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Bioconductor |
PMID:31505654 | Free, Available for download, Freely available | biotools:ascend | https://bio.tools/ascend | SCR_017257 | SciCrunch Registry | Normalization and Differential expression, ASCEND, Analysis of Single Cell Expression | 2026-09-26 02:15:56 | 2 | ||||||
|
IQ-TREE Resource Report Resource Website 1000+ mentions |
IQ-TREE (RRID:SCR_017254) | data analysis software, data processing software, software application, software resource | Software tool as stochastic algorithm for estimating maximum likelihood phylogenies. Used for phylogenomic inference. | stochastic, algorithm, estimate, maximum, likelihood, phylogeny, phylogenomic, inference, data, dataset, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Vienna; Vienna; Austria |
Austrian Science Fund ; University of Vienna |
PMID:25371430 | Free, Available for download, Freely available | biotools:ufboot2 | https://bio.tools/ufboot2/ | SCR_017254 | SciCrunch Registry | 2026-09-26 02:15:59 | 1007 | ||||||
|
EMBOSSMatcher Resource Report Resource Website 10+ mentions |
EMBOSSMatcher (RRID:SCR_017252) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Software tool for pairwise sequence alignment. Identifies local similarities in two input sequences. One of EMBL-EBI search and sequence analysis tools. | pairwise, sequence, alignment, identify, local, similarity, two, input, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools |
EMBL | PMID:30976793 | Free, Freely available | biotools:ebi_search | https://bio.tools/ebi_search | SCR_017252 | SciCrunch Registry | EMBOSS Matcher, emboss_matcher, EMBOSS_Matcher | 2026-09-26 02:15:56 | 16 | |||||
|
proMODMatcher Resource Report Resource Website 1+ mentions |
proMODMatcher (RRID:SCR_017219) | data analysis software, data processing software, software application, software resource | Software tool as probabilistic multi omics data matching procedure to curate data, identify and correct data annotation and errors in large databases. Used to check potential labeling errors in profiles where number of cis relationships is small, such as miRNA and RPPA profiles. | probabilistic, matching, curate, omic, data, identify, correct, error, large, database, analysis, sample, label, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Icahn School of Medicine at Mount Sinai; New York; USA |
NHGRI U01 HG008451; NIAID U19 AI118610; NIA R01 AG046170 |
biotools:modmatcher | https://bio.tools/modmatcher | SCR_017219 | SciCrunch Registry | probabilisticMulti Omics DataMatcher | 2026-09-26 02:15:56 | 1 | |||||||
|
DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
Development Grants For Research Institutions – KRIPIS ; European Regional Development Fund ; European Social Fund ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; John S. Latsis Public Benefit Foundation |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/, http://www.microrna.gr/miRPathv3, https://bio.tools/diana-mirpath | http://www.microrna.gr/miRPathv2 | SCR_017354 | SciCrunch Registry | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-09-26 02:16:00 | 424 | ||||
|
PIRATE Resource Report Resource Website 10+ mentions |
PIRATE (RRID:SCR_017265) | data analysis software, data processing software, software application, software resource | Software pangenomics toolbox for clustering diverged orthologues in bacteria. Used to identify and classify orthologous gene families in bacterial pangenomes over wide range of sequence similarity thresholds. | Pangenome, clustering, genomics, bacteria, orthologue, gene, sequence, amino acid, nucleotide, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/598391 | Free, Available for download, Freely available | biotools:PIRAtE | https://bio.tools/PIRATE | SCR_017265 | SciCrunch Registry | Pangenome Iterative Refinement And Threshold Evaluation | 2026-09-26 02:15:56 | 23 | ||||||
|
GeneMarkS-T Resource Report Resource Website 100+ mentions |
GeneMarkS-T (RRID:SCR_017648) | data analysis software, data processing software, software application, software resource | Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. | Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Georgia Institute of Technology; Georgia; USA |
NHGRI HG000783 | PMID:25870408 | Restricted | biotools:GeneMarkS-t | https://bio.tools/GeneMarkS-T | SCR_017648 | SciCrunch Registry | 2026-09-26 02:16:01 | 172 | ||||||
|
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 | SciCrunch Registry | 2026-09-26 02:16:03 | 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 | SciCrunch Registry | 2026-09-26 02:16:01 | 4 | ||||||||
|
PEMA Resource Report Resource Website 1+ mentions |
PEMA (RRID:SCR_017676) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | SciCrunch Registry | Pipeline for Environmental DNA Metabarcoding Analysis | 2026-09-26 02:16:04 | 1 | ||||||
|
FastProject Resource Report Resource Website |
FastProject (RRID:SCR_017462) | data analysis software, data processing software, data visualization software, software application, software resource | 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 |
California Research Alliance by BASF ; National Institutes of Health NRSA Trainee appointment ; NHGRI U01 HG007910; NIMH U01 MH105979 |
PMID:27553427 | Free, Available for download, Freely available | biotools:fastproject | https://bio.tools/fastproject | SCR_017462 | SciCrunch Registry | 2026-09-26 02:15:59 | 0 | ||||||
|
Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, 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 |
NCI U24 CA224260; NHLBI U54 HL127624; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | SciCrunch Registry | 2026-09-26 02:16:03 | 6 | ||||||
|
Mousebytes Resource Report Resource Website 1+ mentions |
Mousebytes (RRID:SCR_017904) | data or information resource, data repository, database, service resource, storage 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 |
Alzheimer’s Society of Canada ; Brain Canada ; Canadian First Research Excellence Fund (BrainsCAN) ; Canadian Institute of Health Research ; NSERC ; Weston Brain Institute (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 | SciCrunch Registry | MouseBytes | 2026-09-26 02:16:04 | 4 | |||||
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YASARA Resource Report Resource Website 100+ mentions |
YASARA (RRID:SCR_017591) | YASARA | 3d visualization software, data processing software, data visualization software, simulation software, software application, software resource | 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 | SciCrunch Registry | Yasara, Yet Another Scientific Artificial Reality Application | 2026-09-26 02:16:00 | 202 | ||||||
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AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | analysis service resource, data or information resource, database, production service resource, 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 |
Department of Health and Human Services ; NIDA ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | SciCrunch Registry | 2026-09-26 02:16:03 | 8 | ||||||
|
4See Resource Report Resource Website 1+ mentions |
4See (RRID:SCR_018014) | data processing software, data visualization software, software application, 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 | SciCrunch Registry | 2026-09-26 02:16:02 | 1 | |||||||
|
ShinyLearner Resource Report Resource Website 1+ mentions |
ShinyLearner (RRID:SCR_017608) | data analysis software, data processing 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 | SciCrunch Registry | 2026-09-26 02:16:00 | 2 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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