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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
TreeDyn
 
Resource Report
Resource Website
100+ mentions
TreeDyn (RRID:SCR_015946) software application, data processing software, data visualization software, software resource Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. tree, variable, annotation, metainfo, newick, topology, graphic, operator, projection, localization, reflection, leaf, label, bio.tools is listed by: bio.tools
is listed by: Debian
THIS RESOURCE IS NO LONGER IN SERVICE biotools:treedyn https://bio.tools/treedyn SCR_015946 2026-02-16 09:48:55 355
SC3
 
Resource Report
Resource Website
10+ mentions
SC3 (RRID:SCR_015953) software application, data processing software, sequence analysis software, data analysis software, software resource Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients. scRNA-seq, interactive, cluster, clustering, cell, single, rna, rnaseq, bio.tools is listed by: Debian
is listed by: bio.tools
Wellcome Trust 104710/Z/14/Z;
Belgian Network DYSCO ;
FRS-FNRS ;
Belgian State Science Policy Office ;
ARC (Action de Recherche Concerte) ;
Wallonia-Brussels Federation ;
EPSRC EP/N014529/1;
Sanger Institute ;
University of Edinburgh ;
Bloodwise 13003;
MRC ;
Kay Kendall Leukaemia Fund ;
Cambridge NIHR Biomedical Research Center ;
Cambridge Experimental Cancer Medicine Centre ;
Leukemia and Lymphoma Society of America 07037
PMID:28346451 Free, Available for download biotools:sc3 https://bio.tools/sc3 SCR_015953 SC3 package, Single-Cell Consensus Clustering 2026-02-16 09:48:58 20
Canu
 
Resource Report
Resource Website
1000+ mentions
Canu (RRID:SCR_015880) software application, data processing software, sequence analysis software, data analysis software, software resource Software for scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Canu is a fork of the Celera Assembler and is designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). long-read, assembly, k-mer, weighting, repeat separation, adaptive, pacbio, single-molecule, sequencing, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
is related to: Celera assembler
National Human Genome Research Institute ;
US Department of Homeland Security (DHS) HSHQDC-07-C-00020;
National Science Foundation NSF IOS-1237993
PMID:28298431
DOI:10.1101/071282
Free, Available for download biotools:canu, OMICS_14592 http://canu.readthedocs.io/en/latest/
https://bio.tools/canu
https://sources.debian.org/src/canu/
SCR_015880 2026-02-16 09:48:54 2255
Genesis
 
Resource Report
Resource Website
1000+ mentions
Genesis (RRID:SCR_015775) software application, data processing software, data visualization software, data analysis software, software resource Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments. cluster analysis, microarray data, java, gene expression, visualization, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
PMID:11836235 Free for academic use, Free for non-profits, Available for download, Runs on Windows, Runs on Mac OS, Runs on Linux biotools:genesis_microarray https://bio.tools/genesis_microarray SCR_015775 Genesis: Cluster analysis of microarray data 2026-02-16 09:48:52 1018
STAR
 
Resource Report
Resource Website
10000+ mentions
STAR (RRID:SCR_004463) software application, data processing software, image analysis software, software resource, alignment software Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays. RNA-seq data, alignment, RNA-seq reads alignment, reference genome, using uncompressed suffix arrays, bio.tools is used by: STARsolo
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
NHGRI U54 HG004557 PMID:23104886
DOI:10.1093/bioinformatics/bts635
biotools:star, OMICS_01254, SCR_015899 https://github.com/alexdobin/STAR
https://bio.tools/star
https://sources.debian.org/src/rna-star/
SCR_004463 Spliced Transcripts Alignment to Reference, Spliced Transcripts Alignment to a Reference (STAR), rna-star, ultrafast universal RNA-seq aligner 2026-02-16 09:46:22 22809
TAGS
 
Resource Report
Resource Website
100+ mentions
TAGS (RRID:SCR_004294) TAGS software application, data processing software, data analysis software, software resource, time-series analysis software Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, enrichment analysis, time series, function, structure, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Tsinghua University; Beijing; China
THIS RESOURCE IS NO LONGER IN SERVICE biotools:tags, nlx_31187 https://bio.tools/tags http://166.111.130.26/member/yliu/TAGS/ SCR_004294 2026-02-16 09:46:15 139
BSRD
 
Resource Report
Resource Website
10+ mentions
BSRD (RRID:SCR_004249) BSRD data repository, database, storage service resource, service resource, data or information resource A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets. srna target, srna, small regulatory non-coding rna, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Chinese University of Hong Kong; Hong Kong; China
PMID:23203879 Acknowledgement requested, The community can contribute to this resource biotools:bsrd, OMICS_01533 https://bio.tools/bsrd SCR_004249 BSRD - Bacterial Small Regulatory RNA Database, Bacterial Small Regulatory RNA Database 2026-02-16 09:46:14 29
NCBI BioSystems Database
 
Resource Report
Resource Website
100+ mentions
NCBI BioSystems Database (RRID:SCR_004690) BioSystems data analysis service, analysis service resource, data repository, database, storage service resource, production service resource, service resource, data or information resource Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools is listed by: re3data.org
is listed by: Debian
is listed by: bio.tools
is related to: KEGG
is related to: NCBI Structure
is related to: BioCyc
is related to: EcoCyc
is related to: MetaCyc
is related to: Reactome
is related to: Pathway Interaction Database
is related to: WikiPathways
is related to: Gene Ontology
has parent organization: NCBI
NIH PMID:19854944 r3d100011033, biotools:biosystems, nlx_69646 https://bio.tools/biosystems
https://doi.org/10.17616/R31K80
SCR_004690 BioSystems Database, NCBI BioSystems 2026-02-16 09:46:23 118
QuickGO
 
Resource Report
Resource Website
500+ mentions
QuickGO (RRID:SCR_004608) QuickGO web service, controlled vocabulary, data access protocol, database, software resource, ontology, data or information resource A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services. gene, ontology, annotation, browser, visualization, search engine, slimmer-type tool, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, windows, mac os x, linux, unix, gold standard, bio.tools is listed by: OMICtools
is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: STRAP
has parent organization: European Bioinformatics Institute
BBSRC BB/E023541/1 PMID:19744993
PMID:20157483
Apache License, v2, Free for academic use biotools:quickgo, nlx_60318, OMICS_02276 https://bio.tools/quickgo SCR_004608 Quick GO 2026-02-16 09:46:27 523
Small Molecule Pathway Database
 
Resource Report
Resource Website
50+ mentions
Small Molecule Pathway Database (RRID:SCR_004844) SMPDB data analysis service, analysis service resource, database, image, production service resource, service resource, data or information resource An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable. metabolomics, transcriptomics, proteomics, systems biology, small molecule, pathway, human, metabolic pathway, metabolic disease pathway, metabolite signaling pathway, drug-action pathway, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
is related to: ConsensusPathDB
has parent organization: University of Alberta; Alberta; Canada
Genome Alberta ;
Genome Canada
PMID:19948758 nlx_143926, biotools:smpdb, r3d100012753 https://bio.tools/smpdb
https://doi.org/10.17616/R3TB93
SCR_004844 SMPDB (The Small Molecule Pathway Database), Small Molecule Pathway Database (SMPDB) 2026-02-16 09:46:20 95
NCBI Probe
 
Resource Report
Resource Website
10+ mentions
NCBI Probe (RRID:SCR_004816) NCBI Probe data repository, database, storage service resource, service resource, data or information resource Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database. reagent, probe, registry, nucleic acid, gene expression, gene mapping, gene silencing, dna data bank, nucleic acid probe, gold standard, bio.tools is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: UniSTS
has parent organization: NCBI
Public, The community can contribute to this resource nlx_80513, r3d100010780, biotools:ncbi_dbprobe http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe
https://bio.tools/ncbi_dbprobe
https://doi.org/10.17616/R3D041
SCR_004816 NCBI Probe Database, Entrez Probe Database, ProbeDB, Probe Database, dbProbe 2026-02-16 09:46:24 17
European Genome phenome Archive
 
Resource Report
Resource Website
500+ mentions
European Genome phenome Archive (RRID:SCR_004944) EGA web service, data set, data access protocol, data repository, software resource, storage service resource, service resource, data or information resource Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication. phenomenon, trait, sequence, genotype, experiment, case-control, population, family study, snp, cnv, phenotype, genomic, gold standard, bio.tools is used by: Blueprint Epigenome
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: European Bioinformatics Institute
PMID:34791407 Restricted BioTools:ega, biotools:ega, r3d100011242, OMICS_01028, nlx_91316 https://ega-archive.org/
https://bio.tools/ega
https://bio.tools/ega
https://doi.org/10.17616/R3W619
SCR_004944 , The European Genome-phenome Archive, The European Genome-phenome Archive (EGA), EGA 2026-02-16 09:46:21 605
SINA
 
Resource Report
Resource Website
100+ mentions
SINA (RRID:SCR_005067) SINA data analysis service, analysis service resource, software resource, production service resource, service resource Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation. alignment, taxonomic classification, rrna, gene sequence, fasta, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: SILVA
is related to: ARB project
has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany
PMID:22556368 Free, Available for download, Freely available OMICS_01438, biotools:sina https://bio.tools/sina
https://sources.debian.org/src/sina/
https://github.com/epruesse/SINA
SCR_005067 SINA Alignment Service, SILVA Incremental Aligner 2026-02-16 09:46:22 369
Avogadro
 
Resource Report
Resource Website
1000+ mentions
Avogadro (RRID:SCR_015983) software application, data processing software, software toolkit, data visualization software, data analysis software, software resource Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. semantic, optimization, crystallography, chemical, editor, visualization, analysis, molecular, modeling, drug, design, biomolecule, simulation, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
Engineering Research Development Center W912HZ-11-P-0019;
NSF DMR-1005413
PMID:22889332
DOI:10.1186/1758-2946-4-17
Open source, Free, Free to download OMICS_04967, biotools:avogadro http://avogadro.openmolecules.net/
https://github.com/avogadro
https://bio.tools/avogadro
https://sources.debian.org/src/axe-demultiplexer/
SCR_015983 2026-02-16 09:48:55 1965
Bio-tradis
 
Resource Report
Resource Website
50+ mentions
Bio-tradis (RRID:SCR_015993) TraDIS:Transposon Directed Insertion Sequencing software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. software, tool, analysis, data, sequencing, insertion, transponson, direct, mutant, library, perl, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
Wellcome Trust WT098051;
Alexander von Humboldt Stiftung/Foundation ;
Medical Research Council G1100100/1
PMID:26794317
DOI:10.1093/bioinformatics/btw022
Free, Available for download, Freely available OMICS_11083, biotools:bio-tradis https://bio.tools/bio-tradis
https://sources.debian.org/src/bio-tradis/
SCR_015993 2026-02-16 09:48:55 51
Barrnap
 
Resource Report
Resource Website
500+ mentions
Barrnap (RRID:SCR_015995) software application, data processing software, sequence analysis software, data analysis software, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. multithreading, fasta, sequencing, software, predict, location, ribosomal, gene, genome, RNA, prediction, bacteria, archaea, mitochondria, eukaryote, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: OMICtools
THIS RESOURCE IS NO LONGER IN SERVICE biotools:barrnap, OMICS_13988 https://github.com/tseemann/barrnap
https://bio.tools/barrnap
https://sources.debian.org/src/barrnap/
SCR_015995 Barrnap: Basic rapid ribosomal RNA predictor 2026-02-16 09:48:55 568
HyPhy
 
Resource Report
Resource Website
1000+ mentions
HyPhy (RRID:SCR_016162) software application, data processing software, software toolkit, sequence analysis software, data analysis software, software resource Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning. analysis, genetic, sequence, multiply, alignment, rate, pattern, data, evolution, platform, python, r, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
NSF DBI-0096033;
NSF DEB-9996118;
NIH R01 AI47745;
NIH U01 AI43638;
University of California Universitywide AIDS Research Program IS02-SD-701;
University of California ;
San Diego Center for AIDS Research/NIAID Developmental Award 2 P30 AI36214;
NIGMS R01
PMID:15509596 Free, Available for download, Freely available SCR_016271, biotools:HyPhy, OMICS_04235 https://sources.debian.org/src/hyphy-pt/
https://veg.github.io/hyphy-site/
https://github.com/veg/hyphy
https://bio.tools/HyPhy
SCR_016162 HyPhy:Hypothesis Testing using Phylogenies, Hyphy-pt 2026-02-16 09:48:58 1497
Fastml
 
Resource Report
Resource Website
100+ mentions
Fastml (RRID:SCR_016092) web application, data access protocol, software resource, web service Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences. ancestral, amino-acid, sequence, reconstruction, phylogenetic, relation, accurate, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
Israel Science Foundation 878/09;
Bioinformatics Center at Tel-Aviv University
PMID:22661579 Free, Freely available biotools:fastml, OMICS_08650 https://bio.tools/fastml
https://sources.debian.org/src/fastml/
SCR_016092 The FastML Server 2026-02-16 09:48:57 109
BioPlex
 
Resource Report
Resource Website
1000+ mentions
BioPlex (RRID:SCR_016144) data repository, database, storage service resource, service resource, data or information resource Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection. cell, line, protein, immunopurification, mass, spectrometry, interaction, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Harvard Medical School; Massachusetts; USA
NHGRI U41HG006673;
NIDDK K01 DK098285;
Canadian Institutes for Health Research
PMID:28514442 biotools:bioplex_2.0 https://bio.tools/bioplex_2.0 SCR_016144 BioPlex (biophysical interactions of ORFeome-based complexes), Harvard BioPlex, Biophysical Interactions of Orfeome-based comPLEXes (BioPLEX) 2026-02-16 09:48:58 1355
mentha
 
Resource Report
Resource Website
100+ mentions
mentha (RRID:SCR_016148) software application, data processing software, data analysis software, software resource, database, web application, data or information resource Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. protein, ppi, imex, interactome, archival, bio.tools, FASEB list uses: PSICQUIC Registry
is listed by: Debian
is listed by: bio.tools
is related to: IMEx - The International Molecular Exchange Consortium
PMID:23900247 biotools:mentha, r3d100011124 https://bio.tools/mentha
https://doi.org/10.17616/R3SP8V
SCR_016148 2026-02-16 09:48:58 149

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