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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
NanoAmpli-Seq
 
Resource Report
Resource Website
1+ mentions
NanoAmpli-Seq (RRID:SCR_016710) sequence analysis software, data processing software, data analysis software, software application, software resource Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing. amplicon, sequencing, 16S rRNA, mixed, microbial, communities, nanopore, platform, gene is related to: INC-Seq
has parent organization: University of Glasgow; Glasgow; United Kingdom
EPSRC EP/M016811/1;
NERC NE/L011956/1
DOI:10.1101/244517 Free, Available for download, Freely available https://www.protocols.io/view/nanoampli-seq-bioinformatics-workflow-u25eyg6 SCR_016710 2026-02-14 02:03:08 1
Libra
 
Resource Report
Resource Website
Libra (RRID:SCR_016608) sequence analysis software, data processing software, data analysis software, data analytics software, software application, software resource Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples. gene, distance, matrix, computation, k-mer-based, sequence, comparison, Hadoop, metagenomic, sample, bio.tools is listed by: bio.tools
is listed by: Debian
NSF 1640775 Free, Available for download, Freely available biotools:Libra_k-mer https://bio.tools/Libra_k-mer SCR_016608 2026-02-14 02:03:18 0
dCAS
 
Resource Report
Resource Website
dCAS (RRID:SCR_016612) dCAS software resource, web application Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. automate, large, scale, cDNA, sequence, analysis, BLAST, database, gene is listed by: NIAID THIS RESOURCE IS NO LONGER IN SERVICE SCR_016612 Desktop cDNA Annotation System 2026-02-14 02:03:18 0
clusterProfiler
 
Resource Report
Resource Website
10000+ mentions
clusterProfiler (RRID:SCR_016884) data visualization software, data processing software, data analysis software, software application, software resource Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. data, statistical, analysis, visualization, gene, cluster, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is related to: R Project for Statistical Computing
National 973 Projects of China ;
2007 Chang-Jiang Scholars Program ;
National Natural Science Foundation of China ;
Guangdong Natural Science Research Grant ;
Fundamental Research Funds for the Central Universities
PMID:22455463 Free, Available for download, Freely available biotools:clusterprofiler https://github.com/GuangchuangYu/clusterProfiler
https://guangchuangyu.github.io/software/clusterProfiler/
https://bio.tools/clusterprofiler
SCR_016884 Cluster Profiler 2026-02-14 02:03:20 10762
PICRUSt
 
Resource Report
Resource Website
10+ mentions
PICRUSt (RRID:SCR_016855) PICRUSt software resource, simulation software, software application Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome. predict, metagenome, functional, content, DNA, sample, marker, gene, sequence, data, microbiome, 16S, RNA is related to: PICRUSt2 Canadian Institutes of Health Research ;
Canada Research Chairs program ;
Howard Hughes Medical Institute ;
NIDDK P01 DK078669;
NHGRI U01 HG004866;
NHGRI R01 HG004872;
Crohn’s and Colitis Foundation of America ;
Sloan Foundation ;
NHGRI R01 HG005969;
NSF CAREER DBI1053486;
ARO W911NF1110473
PMID:23975157 Free, Available for download, Freely available SCR_016856 SCR_016855 Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, PICRUSt 2026-02-14 02:03:20 36
Stemformatics
 
Resource Report
Resource Website
1+ mentions
Stemformatics (RRID:SCR_017002) portal, data set, data or information resource, organization portal, service resource Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others. gene, expression, data, stem, cell, community, microarray, RNA, sequencing, dataset, cluster ARC Special Research Initiative to Stem Cells Australia ;
ARC Discovery Project ;
ARC Future Fellowship ;
JEM Research Foundation philanthropic funding ;
QLD Government Smart Futures Fellowship ;
University of Melbourne Centre for Stem Cell Systems
PMID:23466562 Free, Available for download, Freely available SCR_017002 2026-02-14 02:03:07 1
Haystack
 
Resource Report
Resource Website
1+ mentions
Haystack (RRID:SCR_017087) data processing software, data analysis software, software toolkit, software application, software resource Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline. epigenetic, variability, cell, plasticity, chromatin, transcription, factor, motif, structure, gene, regulation, analysis is related to: Python Programming Language
has parent organization: Harvard University; Cambridge; Massachusetts
Free, Available for download, Freely available https://github.com/pinellolab/haystack_bio SCR_017087 haystack, haystack_bio 2026-02-14 02:03:23 3
LIMMA
 
Resource Report
Resource Website
10000+ mentions
LIMMA (RRID:SCR_010943) LIMMA data analysis software, software resource, data processing software, software application Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. analysis, gene, expression, microarray, data, linear, model, bio.tools is used by: Glimma
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: GEO2R
is related to: Bioconductor
Free, Available for download, Freely available biotools:limma, OMICS_00769 https://omictools.com/limma-tool
https://bio.tools/limma
https://sources.debian.org/src/r-bioc-limma/
SCR_010943 Linear Models for Microarray Data 2026-02-14 02:02:08 24583
Mouse Genome Informatics (MGI)
 
Resource Report
Resource Website
1000+ mentions
Mouse Genome Informatics (MGI) (RRID:SCR_006460) MGI data or information resource, database International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority uses: InterMOD
is used by: NIF Data Federation
is used by: Resource Identification Portal
is used by: PhenoGO
is used by: Integrated Animals
is used by: Cytokine Registry
is used by: NIH Heal Project
is recommended by: Resource Identification Portal
is recommended by: NIDDK Information Network (dkNET)
is recommended by: National Library of Medicine
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: 3DVC
is listed by: re3data.org
is listed by: OMICtools
is listed by: NIH Data Sharing Repositories
is listed by: InterMOD
is listed by: Resource Information Network
is affiliated with: InterMOD
is related to: MONARCH Initiative
is related to: MouseCyc
is related to: AmiGO
is related to: Gene Expression Database
is related to: Bgee: dataBase for Gene Expression Evolution
is related to: HomoloGene
is related to: Rat Gene Symbol Tracker
is related to: Enhancer Trap Line Browser
is related to: Integrated Brain Gene Expression
is related to: MalaCards
is related to: Gene Ontology
is related to: BioMart Project
is related to: NIH Data Sharing Repositories
is related to: RIKEN integrated database of mammals
is related to: JAX Neuroscience Mutagenesis Facility
is related to: PhenoGO
is related to: International Mouse Strain Resource
is related to: Mouse Genome Database
is related to: Mouse Tumor Biology Database
has parent organization: Jackson Laboratory
is parent organization of: Anatomy of the Laboratory Mouse
is parent organization of: Mouse Genome Informatics Transgenes
is parent organization of: Federation of International Mouse Resources
is parent organization of: MGI GO Browser
is parent organization of: Recombinase (cre) Activity
is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project
is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource
is parent organization of: MGI strains
is parent organization of: MPO
is parent organization of: Phenotypes and Mutant Alleles
is parent organization of: Human Mouse Disease Connection
is parent organization of: Functional Annotation
is parent organization of: Strains, SNPs and Polymorphisms
is parent organization of: Vertebrate Homology
is parent organization of: Batch Data and Analysis Tool
is parent organization of: Nomenclature
NHGRI HG000330;
NHGRI HG002273;
NICHD HD033745;
NCI CA089713
PMID:19274630
PMID:18428715
Free, Freely available nif-0000-00096, OMICS_01656, r3d100010266 http://www.informatics.jax.org/batch
http://www.informatics.jax.org/submit.shtml
http://www.informatics.jax.org/expression.shtml
https://doi.org/10.17616/R35P54
SCR_006460 , MGI, Mouse Genome Informatics 2026-02-14 02:05:55 1119
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
 
Resource Report
Resource Website
10+ mentions
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) GOEAST data analysis service, production service resource, service resource, analysis 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) 2026-02-14 02:06:34 38
DisGeNET
 
Resource Report
Resource Website
1000+ mentions
DisGeNET (RRID:SCR_006178) DisGeNET data or information resource, database Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature. gene, disease, gene-disease association, gene-disease ontology, gene-disease text mining, text mining, genotype-phenotype, rdf, genotype, phenotype, gene-disease, variant-disease, FASEB list uses: Comparative Toxicogenomics Database (CTD)
uses: Genetic Association Database
uses: UniProt
uses: Mouse Genome Database
uses: Reactome
uses: Unified Medical Language System
uses: Entrez Gene
uses: MEDLINE
uses: National Center for Biomedical Ontology
uses: National Cancer Institute Thesaurus
uses: Human Phenotype Ontology
uses: Semanticscience Integrated Ontology
uses: Cytoscape
uses: Literature-derived human gene-disease network
uses: Rat Genome Database (RGD)
uses: National Library of Medicine
uses: PsyGeNET
is used by: HmtPhenome
is listed by: 3DVC
is affiliated with: Gene-Disease Association Type Ontology
has parent organization: Pompeu Fabra University; Barcelona; Spain
EFPIA ;
Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional ;
Elixir-Excelerate ;
Innovative Medicines Initiative Joint Undertaking ;
European Union Seventh Framework Programme ;
European Union Horizon 2020
PMID:27924018
PMID:25877637
PMID:21695124
PMID:20861032
Restricted nlx_151710, r3d100013301 https://doi.org/10.17616/R31NJMR9 SCR_006178 database of gene disease associations 2026-02-14 02:06:33 2210
SNPedia
 
Resource Report
Resource Website
50+ mentions
SNPedia (RRID:SCR_006125) SNPedia data or information resource, database Wiki investigating human genetics including information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA. It is based on a wiki model in order to foster communication about genetic variation and to allow interested community members to help it evolve to become ever more relevant. As the cost of genotyping (and especially of fully determining your own genomic sequence) continues to drop, we''''ll all want to know more - a lot more - about the meaning of these DNA variations and SNPedia will be here to help. SNPedia has been launched to help realize the potential of the Human Genome Project to connect to our daily lives and well-being. For more information see the Wikipedia page, http://en.wikipedia.org/wiki/SNPedia * Download URL: http://www.SNPedia.com/index.php/Bulk * Web Service URL: http://bots.SNPedia.com/api.php dna, genetics, gene, genome, genoset, genotype, medicine, medical condition, genetic variation, dna, genetic variation, genomics, single nucleotide polymorphism, medical association, phenotypic association, genealogical association, variation, genome annotation, phenotype, web service, bio.tools, FASEB list is listed by: Debian
is listed by: bio.tools
PMID:22140107 Creative Commons Attribution-NonCommercial-ShareAlike License, v3 biotools:snpedia, grid.465250.0, nlx_151604 https://ror.org/0253rdk33
https://bio.tools/snpedia
SCR_006125 2026-02-14 02:05:59 62
PANOGA
 
Resource Report
Resource Website
1+ mentions
PANOGA (RRID:SCR_006242) PANOGA data analysis service, production service resource, service resource, analysis service resource A web server to devise functionally important pathways through the identification of single nucleotide polymorphism (SNP)-targeted genes within these pathways. The strength of the methodology stems from its multidimensional perspective, where evidence from the following five resources is combined: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways. single nucleotide polymorphism, genome-wide association study, pathway, function, gene, genetic association, protein-protein interaction network, linkage disequilibrium, protein-protein interaction is listed by: OMICtools
has parent organization: Sabanci University; Istanbul; Turkey
PMID:24413675 Free, Public, Free for academic use, (source code upon request) OMICS_02238 SCR_006242 Pathway and Network-Oriented GWAS Analysis, Pathway and Network Oriented GWAS (Genome-Wide Association Study) Analysis, Pathway and Network Oriented GWAS Analysis 2026-02-14 02:06:33 7
ProPortal
 
Resource Report
Resource Website
1+ mentions
ProPortal (RRID:SCR_006112) ProPortal data or information resource, database ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. Our goal is to provide a source of cross-referenced data across multiple scales of biological organization--from the genome to the ecosystem--embracing the full diversity of ecotypic variation within this microbial taxon, its sister group, Synechococcus and phage that infect them. The site currently contains the genomes of 13 Prochlorococcus strains, 11 Synechococcus strains and 28 cyanophage strains that infect one or both groups. Cyanobacterial and cyanophage genes are clustered into orthologous groups that can be accessed by keyword search or through a genome browser. Users can also identify orthologous gene clusters shared by cyanobacterial and cyanophage genomes. Gene expression data for Prochlorococcus ecotypes MED4 and MIT9313 allow users to identify genes that are up or downregulated in response to environmental stressors. In addition, the transcriptome in synchronized cells grown on a 24-h light-dark cycle reveals the choreography of gene expression in cells in a ''natural'' state. Metagenomic sequences from the Global Ocean Survey from Prochlorococcus, Synechococcus and phage genomes are archived so users can examine the differences between populations from diverse habitats. Finally, an example of cyanobacterial population data from the field is included. genomic, metagenomic, transcriptomic, field data, marine cyanobacterium, genome, ecosystem, ecotypic variation, microbial taxon, phage, genome, gene, orthologous gene cluster, cyanobacteria, cyanophage genome, population dynamics, microarray, metagenome, protein, cyanophage, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
NSF OCE-0425602;
NSF EF0424599;
DOE DE-FG02-02ER63445;
DOE DE-FG02-08ER64516;
DOE DE-FG02-07ER64506;
Gordon and Betty Moore Foundation award letter 495.01
PMID:22102570 Public nlx_151586, biotools:proportal https://bio.tools/proportal SCR_006112 Prochlorococcus Portal 2026-02-14 02:06:25 9
StemCellDB
 
Resource Report
Resource Website
1+ mentions
StemCellDB (RRID:SCR_006305) hES Cell Database data or information resource, database Database characterizing and comparing pluripotent human stem cells. The growth and culture conditions of all 21 human embryonic stem cell lines approved under the August 2001 Presidential Executive Order have been analyzed. Available to the scientific community are the results of our rigorous characterization of these cell lines at a more advanced level. human pluripotent stem cell, human embryonic stem cell line, gene expression, pluripotent, adult, affymetrix microarray platform, agilent microarray platform, gene, stem cell, affymetrix, agilent, microarray, snp, array cgh, methylation, mirna array has parent organization: National Institutes of Health NINDS PMID:23117585 Public nlx_151996 SCR_006305 NIH Stem Cell Database 2026-02-14 02:05:55 1
Clinical Genomic Database
 
Resource Report
Resource Website
1+ mentions
Clinical Genomic Database (RRID:SCR_006427) CGD data or information resource, database Manually curated database of all conditions with known genetic causes, focusing on medically significant genetic data with available interventions. Includes gene symbol, conditions, allelic conditions, inheritance, age in which interventions are indicated, clinical categorization, and general description of interventions/rationale. Contents are intended to describe types of interventions that might be considered. Includes only single gene alterations and does not include genetic associations or susceptibility factors related to more complex diseases. genomic sequencing, genome, clinical, pediatric, adult human, young human, genomic medicine, whole-genome sequencing, gene, organ system, intervention, gene symbol, condition, allelic condition, clinical categorization, manifestation, inheritance, age group, genetic variant, pathogenic mutation is used by: NIF Data Federation
has parent organization: National Human Genome Research Institute
NHGRI PMID:23696674 Free, Freely available nlx_152872, r3d100012332 https://doi.org/10.17616/R31D3C SCR_006427 Clinical Genomics Database 2026-02-14 02:05:55 9
GeneTerm Linker
 
Resource Report
Resource Website
1+ mentions
GeneTerm Linker (RRID:SCR_006385) GTLinker data analysis service, production service resource, service resource, analysis service resource Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service. gene, functional annotation, function, functional metagroup, p-value, annotation, web service is listed by: OMICtools
is related to: Gene Ontology
is related to: KEGG
is related to: InterPro
has parent organization: Spanish National Research Council; Madrid; Spain
PMID:21949701 Acknowledgement requested OMICS_02227 SCR_006385 GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage 2026-02-14 02:06:00 2
Genotype-IBD Sharing Test
 
Resource Report
Resource Website
100+ mentions
Genotype-IBD Sharing Test (RRID:SCR_006257) GIST software resource, software application, resource Software package to test if a marker can account in part for the linkage signal in its region. There are two versions of the software: Windows and Linux/Unix. identical by descent, genotype, gene, genetic, genomic, unix, ms-windows, linux, linkage disequilibrium, linkage, association is listed by: Genetic Analysis Software
has parent organization: Vanderbilt University; Tennessee; USA
Vanderbilt Diabetes Center ;
NHGRI HG00376;
NIDDK DK62370;
NHGRI N01-HG-15465
PMID:14872409 nlx_154133 http://phg.mc.vanderbilt.edu/content/gist SCR_006257 2026-02-14 02:06:33 120
Magic
 
Resource Report
Resource Website
500+ mentions
Magic (RRID:SCR_006406) MAGIC data or information resource, service resource, database Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Expression Omnibus
is related to: ArrayExpress
is related to: Plant Ontology
is related to: Gene Ontology
has parent organization: Ghent University; Ghent; Belgium
PMID:24407224 biotools:magic, OMICS_02206 https://bio.tools/magic SCR_006406 MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium 2026-02-14 02:06:34 706
Lists2Networks
 
Resource Report
Resource Website
1+ mentions
Lists2Networks (RRID:SCR_006323) L2N data analysis service, production service resource, service resource, analysis service resource A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system. high-throughput sequencing, analysis, gene, protein is listed by: OMICtools
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
PMID:20152038 Free, Public, Account required OMICS_02231 http://www.lists2networks.org SCR_006323 Lists2Networks: Integrated analysis of gene/protein lists 2026-02-14 02:06:26 3

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