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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IgDiscover Resource Report Resource Website 10+ mentions |
IgDiscover (RRID:SCR_024037) | software application, data processing software, data analysis software, software resource | Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze antibody repertoires, discover new V genes, high-throughput sequencing reads, | is listed by: Debian | PMID:27995928 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_16456 | https://sources.debian.org/src/igdiscover/ https://github.com/NBISweden/IgDiscover/ |
SCR_024037 | igdiscover | 2026-02-15 09:23:21 | 10 | ||||||
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BOLT-LMM Resource Report Resource Website 1+ mentions |
BOLT-LMM (RRID:SCR_023978) | software application, data processing software, data analysis software, software resource | Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts. | statistical tool, identifying genetic associations, genome wide association studies, large cohorts, | is listed by: Debian | PMID:25642633 | Free, Available for download, Freely available | OMICS_13504 | https://sources.debian.org/src/bolt-lmm/ | SCR_023978 | bolt-lmm | 2026-02-15 09:22:34 | 2 | ||||||
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IVA Resource Report Resource Website 1+ mentions |
IVA (RRID:SCR_024044) | software application, data processing software, data analysis software, software resource | Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth. | de novo assembler, assemble virus genomes, no repeat sequences, Illumina reads, pairs sequenced from mixed populations, | is listed by: Debian | PMID:25725497 | Free, Available for download, Freely available, | OMICS_08188 | https://sources.debian.org/src/iva/ http://sanger-pathogens.github.io/iva/ |
SCR_024044 | Iterative Virus Assembler - de novo virus assembler of Illumina paired reads., iva | 2026-02-15 09:22:35 | 1 | ||||||
|
CONTRAfold Resource Report Resource Website 1+ mentions |
CONTRAfold (RRID:SCR_023994) | CONTRAfold | software application, simulation software, software resource | Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction. | sequence prediction, | is listed by: Debian | PMID:16873527 | Free, Available for download, Freely available | OMICS_03452 | https://sources.debian.org/src/CONTRAfold/ | SCR_023994 | CONditional TRAining for RNA Secondary Structure Prediction, contrafold | 2026-02-15 09:22:34 | 2 | |||||
|
CodonW Resource Report Resource Website 100+ mentions |
CodonW (RRID:SCR_023989) | software application, data processing software, data analysis software, software resource | Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage. | Multivariate analysis, correspondence analysis, codon and amino acid usage, calculate standard indices, codon usage, | is listed by: Debian | Free, Available for download, Freely available | OMICS_08756 | https://sources.debian.org/src/codonw/ | SCR_023989 | codonw | 2026-02-15 09:23:20 | 193 | |||||||
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EMPeror Resource Report Resource Website 1+ mentions |
EMPeror (RRID:SCR_024013) | web application, software resource | Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets. | visualizing high-throughput microbial community data, | is listed by: Debian | PMID:24280061 | Free, Available for download, Freely available | https://sources.debian.org/src/emperor/ | SCR_024013 | EMPEROR, Emperor, emperor | 2026-02-15 09:23:20 | 6 | |||||||
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EMBOSS explorer Resource Report Resource Website 1+ mentions |
EMBOSS explorer (RRID:SCR_024014) | web application, software resource | Web based graphical user interface to the EMBOSS suite of bioinformatics tools. | graphical user interface, EMBOSS suite, bioinformatics tools, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/emboss-explorer/ | SCR_024014 | emboss-explorer | 2026-02-15 09:23:17 | 1 | ||||||||
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Filtlong Resource Report Resource Website 100+ mentions |
Filtlong (RRID:SCR_024020) | software application, data processing software, software resource | Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter. | filtering long reads by quality, read length, read identity, filtering reads, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/filtlong/ | SCR_024020 | filtlong | 2026-02-15 09:23:17 | 309 | ||||||||
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CTSim Resource Report Resource Website |
CTSim (RRID:SCR_024004) | software application, simulation software, software resource | Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions. | Computed tomography simulator, reconstruct original phantom image from projections, reconstruct image, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctsim/ | SCR_024004 | ctsim, Open Source Computed Tomography Simulator | 2026-02-15 09:23:17 | 0 | ||||||||
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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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GoPubMed Resource Report Resource Website 10+ mentions |
GoPubMed (RRID:SCR_005823) | GoPubMed | data or information resource, database, service resource | A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool | other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: PubMed has parent organization: Biotechnology Center of the TU Dresden |
European Union IST-2004-506779 | PMID:15980585 | Free for academic use | biotools:gopubmed, nlx_149328, OMICS_01183 | https://bio.tools/gopubmed | SCR_005823 | 2026-02-15 09:19:03 | 29 | |||||
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Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | service resource, analysis service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, 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: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-02-15 09:19:13 | 6 | ||||
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PRED-TMBB Resource Report Resource Website 50+ mentions |
PRED-TMBB (RRID:SCR_006190) | PRED-TMBB | service resource, analysis service resource, data analysis service, production service resource | A web tool, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins, and of discriminating such proteins from water-soluble ones when screening large datasets. The model is trained in a discriminative manner, aiming at maximizing the probability of the correct prediction rather than the likelihood of the sequences. The training is performed on a non-redundant database consisting of 16 outer membrane proteins (OMP''s) with their structures known at atomic resolution. We show that we can achieve predictions at least as good comparing with other existing methods, using as input only the amino-acid sequence, without the need of evolutionary information included in multiple alignments. The method is also powerful when used for discrimination purposes, as it can discriminate with a high accuracy the outer membrane proteins from water soluble in large datasets, making it a quite reliable solution for screening entire genomes. This web-server can help you run a discriminating process on any amino-acid sequence and thereafter localize the transmembrane strands and find the topology of the loops. | protein, hidden markov model, prediction, membrane protein, beta-barrel outer membrane protein, gram-negative bacteria, topology, outer membrane protein, beta-barrel protein, probability, transmembrane strand, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
Greek Ministry of National Education and Religious Affairs | PMID:15215419 PMID:15070403 |
Acknowledgement requested | biotools:pred-tmbb, nlx_151734 | https://bio.tools/pred-tmbb | SCR_006190 | PRED-TMBB: A Hidden Markov Model method capable of predicting and discriminating beta-barrel outer membrane proteins | 2026-02-15 09:19:11 | 54 | ||||
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Atlas of Genetics and Cytogenetics in Oncology and Haematology Resource Report Resource Website 10+ mentions |
Atlas of Genetics and Cytogenetics in Oncology and Haematology (RRID:SCR_007199) | atlas, data or information resource, database | Online journal and database devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. Its aim is to cover the entire field under study and it presents concise and updated reviews (cards) or longer texts (deep insights) concerning topics in cancer research and genomics. | gene, cytogenetic, cancer, cancer research, genomic, online journal, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:23161685 | Freely available, Available to the scientific community | nif-0000-30129, biotools:atlasgeneticsoncology | https://bio.tools/atlasgeneticsoncology | SCR_007199 | Genetics and Cytogenetics Atlas | 2026-02-15 09:19:43 | 38 | ||||||
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mitopred Resource Report Resource Website 1+ mentions |
mitopred (RRID:SCR_006135) | MITOPRED | service resource, analysis service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It predicts nuclear-encoded mitochondrial proteins from all eukaryotic species including plants. Prediction is based on the occurrence patterns of Pfam domains (version 16.0) in different cellular locations, amino acid composition and pI value differences between mitochondrial and non-mitochondrial locations. Additionally, you may download MITOPRED predictions for complete proteomes. Re-calculated predictions are instantly accessible for proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Homo sapiens, Mus musculus and Arabidopsis species as well as all the eukaryotic sequences in the Swiss-Prot and TrEMBL databases. Queries, at different confidence levels, can be made through four distinct options: (i) entering Swiss-Prot/TrEMBL accession numbers; (ii) uploading a local file with such accession numbers; (iii) entering protein sequences; (iv) uploading a local file containing protein sequences in FASTA format. The Mitopred algorithm works based on the differences in the Pfam domain occurrence patters and amino acid composition differences in different cellular compartments. Location specific Pfam domains have been determined from the entire eukaryotic set of Swissprot database. Similarly, differences in the amino acid composition between mitochondrial and non-mitochondrial sequences were pre-calculated. This information is used to calculate location-specific amino acid weights that are used to calculate amino acid score. Similarly, pI average values of the N-terminal 25 residues in different cellular location were also determined. This knowledge-base is accessed by the program during execution. | yeast, c. elegans, drosophila, mouse, human, arabidopsis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University at Albany; New York; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mitopred, nif-0000-03956, BioTools:mitopred | https://bio.tools/mitopred https://bio.tools/mitopred https://bio.tools/mitopred |
SCR_006135 | A genome-scale method for predicting mitochondrial proteins | 2026-02-15 09:19:09 | 7 | ||||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | service resource, analysis service resource, data analysis service, production service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-02-15 09:19:13 | 106 | ||||||
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Magic Resource Report Resource Website 500+ mentions |
Magic (RRID:SCR_006406) | MAGIC | data or information resource, database, service resource | 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 | 2026-02-15 09:19:16 | 706 | ||||||
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Hyper Cell Line Database Resource Report Resource Website |
Hyper Cell Line Database (RRID:SCR_007730) | HyperCLDB | material resource, tissue bank, biomaterial supply resource | Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE. | cell, cell line, tumor, tissue, organ, blood, bodily fluid, ascitic fluid, brain, bone marrow, cancer, transforming agent, software, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: ATCC is related to: Cell Line Knowledge Base has parent organization: IST National Institute for Cancer Research; Genoa; Italy |
Cancer, Etc. | PMID:18927105 | nif-0000-03004, biotools:hypercldb | https://bio.tools/hypercldb | SCR_007730 | 2026-02-15 09:19:39 | 0 | ||||||
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IRESite Resource Report Resource Website 10+ mentions |
IRESite (RRID:SCR_007753) | data or information resource, database | Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments. | bio.tools, experimentally verified IRES structures, Internal Ribosome Entry Site segments, IRES structures, IRES segments |
is listed by: bio.tools is listed by: Debian has parent organization: Charles University; Prague; Czech Republic |
nif-0000-03047, nif-0000-03046, SCR_007754, biotools:iresite | https://bio.tools/iresite | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | SCR_007753 | IRESdb, , IRESdb - the Internal Ribosome Entry Site database, Internal Ribosome Entry Site | 2026-02-15 09:19:47 | 45 | |||||||
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Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) Resource Report Resource Website 10+ mentions |
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) | SNPSpD | service resource, analysis service resource, data analysis service, production service resource | SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Queensland Institute of Medical Research |
National Health and MRC Australia 241916 | PMID:14997420 | biotools:snpspd, nif-0000-31985 | https://bio.tools/snpspd | http://genepi.qimr.edu.au/general/daleN/SNPSp | SCR_008621 | Single Nucleotide Polymorphism Spectral Decomposition | 2026-02-15 09:19:52 | 18 |
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