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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
IMGT HighV-QUEST
 
Resource Report
Resource Website
10+ mentions
IMGT HighV-QUEST (RRID:SCR_018196) software application, portal, data processing software, software resource, service resource, alignment software, production service resource, image analysis software, data or information resource, analysis service resource Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing. Next generation sequencing, B cell, T cell, sequence alignment, immunoglobulin, antibody, T cell receptor, analysis, sequence, bio.tools is listed by: bio.tools
is listed by: Debian
NHMRC ;
MESR ;
CNRS ;
Université Montpellier 2 ;
France ;
GENCI
PMID:22647994
PMID:23995877
PMID:22665256
Restricted biotools:IMGt_HighV-QUESt https://bio.tools/IMGT_HighV-QUEST SCR_018196 IMGT/HighV QUEST, IMGT/HighV-QUEST, IMGT web portal 2026-02-15 09:22:11 11
PM4NGS
 
Resource Report
Resource Website
1+ mentions
PM4NGS (RRID:SCR_019164) data management software, software application, data processing software, software resource, workflow software, software toolkit, data analysis software Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution. NGS workflow, standard organizational structure generation, Next Generation Sequencing data, NGS data analysis, NGS data analysis workflow, data integration, Jupyter notebook, CWL format, bio.tools is listed by: bio.tools
is listed by: Debian
Intramural Research Program of the National Library of Medicine NIH DOI:10.7490/f1000research.1117155.1 Free, Freely available biotools:pm4ngs https://bio.tools/pm4ngs SCR_019164 Project Manager for Next Generation Sequencing 2026-02-15 09:22:20 1
ComplexHeatmap
 
Resource Report
Resource Website
1000+ mentions
ComplexHeatmap (RRID:SCR_017270) software application, data visualization software, data processing software, software resource, data analysis software Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools is listed by: Debian
is listed by: bio.tools
German Cancer Research Center-Heidelberg Center for Personalized Oncology ;
BMBF
PMID:27207943 Free, Available for download, Freely available biotools:complexheatmap https://github.com/jokergoo/ComplexHeatmap
https://bio.tools/complexheatmap
SCR_017270 2026-02-15 09:22:00 3266
SWISS-MODEL
 
Resource Report
Resource Website
1000+ mentions
SWISS-MODEL (RRID:SCR_018123) software resource, data access protocol, web service, service resource, data or information resource Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists. 3D protein structure, homology modeling server, protein modeling, structural bioinformatics, automated comparative modeling, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: ExPASy Bioinformatics Resource Portal
is related to: Swiss-PdbViewerDeepViewv4.0
has parent organization: University of Basel; Basel; Switzerland
provides: SWISS-MODEL Repository
PMID:12824332 Free, Freely available biotools:swiss-model_workspace, biotools:swiss_model https://bio.tools/swiss_model
https://bio.tools/swiss-model_workspace
SCR_018123 2026-02-15 09:22:10 2796
SIGNOR
 
Resource Report
Resource Website
10+ mentions
SIGNOR (RRID:SCR_018485) database, service resource, storage service resource, data repository, data or information resource Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles. Signal transduction data, signaling information, published data collection, activity flow, chemical inhibitor, human proteome, manually annotated data, protein, protein relationship, FAIR data, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: REDIportal
Italian Association for Cancer Research ;
ELIXIR-IIB ;
Italian Node of the European ELIXIR infrastructure ;
EMBL-EBI
PMID:31665520 Free, Available for download, Freely available biotools:signor https://bio.tools/signor SCR_018485 SIGnaling Network Open Resource, SIGNOR 2.0 2026-02-15 09:22:15 40
MRIcron
 
Resource Report
Resource Website
1000+ mentions
MRIcron (RRID:SCR_002403) MRIcron software application, data visualization software, data processing software, software resource Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools is used by: XFSL: An FSL toolbox
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: neurodebian
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Colour maps for brain imaging
has parent organization: University of South Carolina; South Carolina; USA
PMID:17583985
PMID:11568431
BSD License biotools:MRIcron, nif-0000-00122 https://sources.debian.org/src/mricron/
http://www.mccauslandcenter.sc.edu/mricro/
http://www.nitrc.org/projects/mricron
http://neuro.debian.net/pkgs/mricron.html
https://bio.tools/MRIcron
SCR_002403 mricron - magnetic resonance image conversion viewing and analysis 2026-02-15 09:18:18 2194
Identifiers.org
 
Resource Report
Resource Website
50+ mentions
Identifiers.org (RRID:SCR_003735) Identifiers.org identifier resolution, service resource, production service resource A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile. identifier, life sciences, bio.tools uses: MIRIAM Resources
is listed by: bio.tools
is listed by: Debian
has parent organization: European Bioinformatics Institute
Free nlx_157931, biotools:identifiers.org https://bio.tools/identifiers.org SCR_003735 2026-02-15 09:18:34 50
INMEX
 
Resource Report
Resource Website
10+ mentions
INMEX (RRID:SCR_004173) INMEX service resource, analysis service resource, data analysis service, production service resource A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
is related to: KEGG
is related to: Human Metabolome Database
has parent organization: University of British Columbia; British Columbia; Canada
Killam Trust ;
Canadian Institutes of Health Research
PMID:23766290 Acknowledgement requested biotools:inmex, OMICS_01546 https://bio.tools/inmex SCR_004173 INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data 2026-02-15 09:18:38 19
VIPERdb
 
Resource Report
Resource Website
50+ mentions
VIPERdb (RRID:SCR_002853) data or information resource, database Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
has parent organization: Scripps Research Institute
PMID:33313778
PMID:30265627
Free, Freely available nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 https://bio.tools/viperdb
https://doi.org/10.17616/R3HT0Q
SCR_002853 Virus Particle ExploreR 2026-02-15 09:18:23 59
Proteome Analyst Specialized Subcellular Localization Server
 
Resource Report
Resource Website
1+ mentions
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) PA-SUB service resource, analysis service resource, data analysis service, production service resource Web server specialized to predict the subcellular localization of proteins using established machine learning techniques. subcellular localization, protein, machine learning, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Alberta; Alberta; Canada
PMID:14990451 Free, Available for download, Freely available biotools:pa-sub, OMICS_01631 https://psort.org/#:~:text=Proteome%20Analyst's%20Subcellular%20Localization%20Server
proteins%20to%20many%20localization%20sites.
SCR_003143 2026-02-15 09:18:29 1
FastSNP
 
Resource Report
Resource Website
50+ mentions
FastSNP (RRID:SCR_003140) service resource, analysis service resource, data analysis service, production service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information. single nucleotide polymorphism, function, phenotype, transcript, prioritize, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Academia Sinica; Taipei; Taiwan
National Research Program in Genomic Medicine ;
National Science Council Taiwan NSC93-3112-B-001-008-Y;
National Science Council Taiwan NSC93-3112-B-001-018-Y
PMID:16845089 Free, Freely available biotools:fastsnp, OMICS_00173, nif-0000-30566 https://bio.tools/fastsnp http://fastsnp.ibms.sinica.edu.tw/pages/input_CandidateGeneSearch.jsp SCR_003140 FastSNP: A Functional Analysis and Selection Tool for SNP in Large Scale Association Study, Function Analysis and Selection Tool for Single Nucleotide Polymorphisms, A Functional Analysis and Selection Tool for SNP in Large Scale Association Study 2026-02-15 09:18:27 62
T-profiler
 
Resource Report
Resource Website
10+ mentions
T-profiler (RRID:SCR_003452) T-profiler service resource, analysis service resource, data analysis service, production service resource One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool expression, gene, binding, cellular, transcriptional, gene expression, microarray, gene ontology, transcription factor, binding motif, chip-chip, chip, motif, t-test, statistical analysis, transcriptome, bio.tools is listed by: Biositemaps
is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: Columbia University; New York; USA
has parent organization: University of Amsterdam; Amsterdam; Netherlands
Netherlands Foundation for Technical Research APB.5504;
NHGRI R01HG003008
PMID:15980543 Free for academic use nif-0000-33354, biotools:t-profiler https://bio.tools/t-profiler SCR_003452 T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data 2026-02-15 09:18:31 11
Distant Regulatory Elements
 
Resource Report
Resource Website
10+ mentions
Distant Regulatory Elements (RRID:SCR_003058) DiRE service resource, analysis service resource, data analysis service, production service resource Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. regulatory element, enhancer identification, genome, prediction, transcription factor binding site, gene, co-expression, co-function, function, transcription factor, comparative genomics, regulatory function, gene locus, chromosome, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: NCBI
NLM ;
Intramural Research Program
PMID:18487623 Free, Freely available nif-0000-30448, biotools:dire https://bio.tools/dire SCR_003058 Distant Regulatory Elements of co-regulated genes 2026-02-15 09:18:26 25
Human Gene Connectome Server
 
Resource Report
Resource Website
1+ mentions
Human Gene Connectome Server (RRID:SCR_002627) HGCS service resource, analysis service resource, data analysis service, production service resource An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways. gene, disease, phenotype, genome, connectome, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Human Gene Connectome
PMID:23509278 Free nlx_156049, biotools:hgcs https://bio.tools/hgcs SCR_002627 2026-02-15 09:18:21 5
MLTreeMap
 
Resource Report
Resource Website
1+ mentions
MLTreeMap (RRID:SCR_004792) MLTreeMap service resource, analysis service resource, data analysis service, production service resource Data analysis service that analyzes DNA sequences and determines their most likely phylogenetic origin. Its main use is in metagenomics projects, where DNA is isolated directly from natural environments and sequenced (the organisms from which the DNA originates are often entirely undescribed). It will search such sequences for suitable marker genes, and will use maximum likelihood analysis to place them in the ''''Tree of Life''''. This placement is more reliable than simply assessing the closest relative of a sequence using BLAST. More importantly, MLTreeMap decides not only who is the closest relative of your query sequence, but also how deep in the tree of life it probably branched off. Additionally, MLTreeMap searches the sequences for genes, which are coding for key enzymes of important functional pathways, such as RuBisCo, methane monooxygenase or nitrogenase. In case of a positive hit, MLTreeMap uses maximum likelihood analysis to place them in the respective ''''gene-family tree''''. phylogeny, gene, fasta, dna sequence, nucleotide sequence, metagenomics, metagenome, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: COG
has parent organization: University of Zurich; Zurich; Switzerland
PMID:20687950 biotools:mltreemap, OMICS_01457 https://bio.tools/mltreemap SCR_004792 Phylogenetic analysis of metagenomics sequence data 2026-02-15 09:18:54 4
AmphoraNet
 
Resource Report
Resource Website
10+ mentions
AmphoraNet (RRID:SCR_005009) AmphoraNet service resource, analysis service resource, data analysis service, production service resource Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample. dna sequence, amino acid sequence, dna, sequence, amino acid, phylogenetic, reliability score, nucleotide, protein, nucleotide sequence, protein sequence, phylogenetic analysis, metagenomic, metagenomics, phylotyping, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Eotvos Lorand University; Budapest; Hungary
PMID:24144838 Acknowledgement requested, Free, Public biotools:amphoranet, OMICS_01450 https://bio.tools/amphoranet SCR_005009 2026-02-15 09:18:53 16
ProfCom - Profiling of complex functionality
 
Resource Report
Resource Website
1+ mentions
ProfCom - Profiling of complex functionality (RRID:SCR_005797) ProfCom service resource, analysis service resource, data analysis service, production service resource Profiling of Complex Functionality (ProfCom) is a web-based tool for the functional interpretation of a gene list that was identified to be related by experiments. A trait which makes ProfCom a unique tool is an ability to profile enrichments of not only available Gene Ontology (GO) terms but also of complex function. A complex function is constructed as Boolean combination of available GO terms. The complex functions inferred by ProfCom are more specific in comparison to single terms and describe more accurately the functional role of genes. Platform: Online tool gene, function, profile, gene ontology, complex function, statistical analysis, bio.tools is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
has parent organization: Institute of Bioinformatics and Systems Biology; Neuherberg; Germany
DFG PMID:16959266 Free for academic use biotools:profcom, nlx_149276 https://bio.tools/profcom SCR_005797 Profiling of Complex Functionality, Profiling of Complex Functionality (ProfCom) 2026-02-15 09:19:03 4
SerbGO
 
Resource Report
Resource Website
SerbGO (RRID:SCR_005798) SerbGO service resource, analysis service resource, data analysis service, production service resource SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool microarray, gene expression, statistical analysis, gene ontology, bio.tools is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: University of Barcelona; Barcelona; Spain
PMID:18480123 Free for academic use nlx_149286, biotools:serbgo https://bio.tools/serbgo SCR_005798 SerbGO - Searching the best GO Tool 2026-02-15 09:19:12 0
Kismeth
 
Resource Report
Resource Website
50+ mentions
Kismeth (RRID:SCR_005444) Kismeth service resource, analysis service resource, data analysis service, production service resource A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. plant, methylation, bisulfite sequencing, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
PMID:18786255 Free for academic use, Contact for commercial use biotools:kismeth, OMICS_00602 https://bio.tools/kismeth SCR_005444 2026-02-15 09:18:58 53
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
 
Resource Report
Resource Website
10+ mentions
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) GOEAST service resource, analysis service resource, data analysis service, production service resource Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool statistical analysis, gene ontology, high-throughput, microarray, hybridization, gene, visualization, bio.tools is listed by: Gene Ontology Tools
is listed by: Debian
is listed by: bio.tools
is related to: Gene Ontology
has parent organization: Chinese Academy of Sciences; Beijing; China
National Natural Science Foundation of China 30725014;
National Natural Science Foundation of China 90612019;
Ministry of Science and Technology of China 2007CB946901;
Chinese Academy of Sciences KSCX2-YW-R-134;
Chinese Academy of Sciences KSCX2-YW-N-024
PMID:18487275 Free for academic use biotools:goeast, nlx_149248 https://bio.tools/goeast SCR_006580 Gene Ontology Enrichment Analysis Software Toolkit, Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) 2026-02-15 09:19:18 38

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