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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DSS Resource Report Resource Website 1+ mentions |
DSS (RRID:SCR_002754) | software toolkit, software library, software resource | Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | standalone software, unix/linux, mac os x, windows, r, differential expression, rna-seq, chip-seq, dna methylation, differential expression, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24561809 | Free, Freely available, Available for download | OMICS_03273 | SCR_002754 | Dispersion Shrinakge for Sequencing data, DSS - Dispersion shrinakge for sequencing data | 2026-08-05 10:43:41 | 8 | |||||||
|
MethDB Resource Report Resource Website 10+ mentions |
MethDB (RRID:SCR_003108) | MethDB | data or information resource, data repository, database, storage service resource, service resource | Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc.. | methylation |
is listed by: OMICtools has parent organization: University of Perpignan Via Domitia; Perpignan; France has parent organization: French National Center for Scientific Research |
PMID:11125109 PMID:17965614 PMID:12163707 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03119, OMICS_01840 | http://www.methdb.net/ | SCR_003108 | DNA Methylation Database, MethDB - the database for DNA methylation and environmental epigenetic effects | 2026-08-05 10:43:46 | 15 | |||||
|
DnaSP Resource Report Resource Website 5000+ mentions |
DnaSP (RRID:SCR_003067) | DnaSP | software resource, data processing software, software application, data analysis software | A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form. | genetics, dna, population genetics, sequence, polymorphism, nucleotide polymorphism, dna sequence, population, noncoding, synonymous, nonsynonymous |
is listed by: OMICtools has parent organization: University of Barcelona; Barcelona; Spain |
Spanish Direccion General de Investigacion Cientifica y Technica PB91-0245; Spanish Direccion General de Investigacion Cientifica y Technica PB94-0923; Spanish Direccion General de Investigacion Cientifica y Technica PB97-0918; Spanish Direccion General de Investigacion Cientifica y Technica TXT98-1802; Spanish Direccion General de Investigacion Cientifica y Technica BMC2001-2906; Spanish Direccion General de Investigacion Cientifica y Technica BFU2004-02253; Spanish Direccion General de Investigacion Cientifica y Technica BFU2007-6292 |
PMID:19346325 PMID:19378153 PMID:14668244 PMID:10089204 PMID:9183537 PMID:8808578 |
Free, Available for download, Freely available | OMICS_01820, nif-0000-30461 | SCR_003067 | DNA Sequence Polymorphism | 2026-08-05 10:43:45 | 5935 | |||||
|
JuncBASE Resource Report Resource Website 10+ mentions |
JuncBASE (RRID:SCR_003103) | software resource, data processing software, software application, data analysis software | Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. | splicing event, splicing events, alternative splicing event, rna seq |
is listed by: OMICtools is hosted by: GitHub |
Free, Available for download, Freely available | OMICS_01335 | https://github.com/anbrooks/juncBASE | SCR_003103 | 2026-08-05 10:43:46 | 19 | ||||||||
|
PredictNLS Resource Report Resource Website 10+ mentions |
PredictNLS (RRID:SCR_003133) | PredictNLS | software resource, data analysis service, production service resource, service resource, analysis service resource | Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given. | bio.tools, nuclear localization signal, protein, protein sequence |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ROSTLAB has parent organization: Columbia University; New York; USA |
DOI:10.1093/embo-reports/kvd092 | Free, Available for download, Freely available | nif-0000-31416, OMICS_01633, SCR_008553, biotools:predictnls | https://www.rdocumentation.org/packages/propagate/versions/1.0-4/topics/predictNLS | SCR_003133 | Prediction and Analysis of Nuclear Localization Signals | 2026-08-05 10:43:46 | 30 | |||||
|
LUMPY Resource Report Resource Website 100+ mentions |
LUMPY (RRID:SCR_003253) | data processing software, software application, simulation software, data analysis software, standalone software, software resource | Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed. | probabilistic, framework, structural, variant, discovery |
is listed by: OMICtools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
NHGRI R01 HG006693; NIH Office of the Director DP2 OD006493; Burroughs Wellcome Fund Career Award |
PMID:24970577 | Free, Available for download, Freely available | OMICS_04674 | https://sources.debian.org/src/lumpy-sv/ | SCR_003253 | lumpy-sv, LUMPY Express | 2026-08-05 10:43:48 | 447 | |||||
|
JETTA Resource Report Resource Website 1+ mentions |
JETTA (RRID:SCR_003091) | JETTA | software resource, data processing software, software application, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study. | exon, exon splicing |
is listed by: OMICtools has parent organization: Stanford University; Stanford; California |
PMID:22433281 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01334 | SCR_003091 | 2026-08-05 10:43:45 | 3 | |||||||
|
SplicingCompass Resource Report Resource Website 1+ mentions |
SplicingCompass (RRID:SCR_003249) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software for detection of differential splicing between two different conditions using RNA-Seq data. | differential splicing, splicing event, exon removal, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23449093 | Free, Available for download, Freely available | biotools:splicingcompass, OMICS_01340 | https://github.com/KoenigLabNM/SplicingCompass | SCR_003249 | Splicing Compass | 2026-08-05 10:43:48 | 2 | ||||||
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PathGuide: the pathway resource list Resource Report Resource Website 10+ mentions |
PathGuide: the pathway resource list (RRID:SCR_003248) | Pathguide | data or information resource, catalog, database | Catalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. | gene interaction network, metabolic pathway, signaling pathway, pathway diagram, protein-compound interaction, protein-protein interaction, protein sequence focused, transcription factor, gene regulatory network, transcription factor target, genetic interaction, pathway, molecular interaction, FASEB list |
is listed by: OMICtools is related to: PSI-MI is related to: bioDBcore is related to: Biological Pathways Exchange is related to: CellML is related to: SBML is related to: Biological Pathways Exchange |
PMID:16381921 | Free, Freely available | SciRes_000148, OMICS_01701, nif-0000-00640 | SCR_003248 | 2026-08-05 10:43:48 | 47 | |||||||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | source code, software resource, data analysis service, production service resource, service resource, analysis service resource | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-08-05 10:43:45 | 1673 | ||||
|
MultiLoc Resource Report Resource Website 10+ mentions |
MultiLoc (RRID:SCR_003151) | MultiLoc | software resource, data analysis service, production service resource, service resource, analysis service resource | An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available. | subcellular localization, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tubingen; Tubingen; Germany |
PMID:19723330 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01628, biotools:multiloc2 | https://bio.tools/multiloc2 | SCR_003151 | 2026-08-05 10:43:46 | 40 | ||||||
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GeneScissors Resource Report Resource Website 1+ mentions |
GeneScissors (RRID:SCR_003146) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software for detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment. | transcriptome inference, read misalignment, rna seq |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA works with: Cufflinks works with: TopHat |
PMID:23812996 | Free, Available for download, Freely available | OMICS_01232 | SCR_003146 | Gene Scissors | 2026-08-05 10:43:46 | 2 | |||||||
|
Primer3 Resource Report Resource Website 10000+ mentions |
Primer3 (RRID:SCR_003139) | Primer3 | software resource, data analysis service, production service resource, service resource, analysis service resource | Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos. | primer, primer design, polymerase chain reaction, pcr primer, dna sequence, c, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Primer3Plus is related to: Primer-BLAST has parent organization: University of Tartu; Tartu; Estonia |
NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:22730293 PMID:17379693 DOI:10.1385/1-59259-192-2:365 DOI:10.1385/1-59259-192-2:365 |
Free, Freely available | nlx_156833, OMICS_02325, biotools:primer3 | http://bioinfo.ut.ee/primer3-0.4.0/, http://sourceforge.net/projects/primer3/, http://frodo.wi.mit.edu/primer3, https://bio.tools/primer3, https://sources.debian.org/src/primer3/, https://sources.debian.org/src/primer3/ | SCR_003139 | Primer3web - Pick primers from a DNA sequence, Primer3 - PCR primer design tool, Primer3web | 2026-08-05 10:43:46 | 10957 | ||||
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Talking Glossary of Genetic Terms Resource Report Resource Website |
Talking Glossary of Genetic Terms (RRID:SCR_003215) | Talking Glossary | data or information resource, training material, narrative resource, database | Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms. | glossary, image, genetic, gene, education |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
NHGRI | The community can contribute to this resource | nlx_156942, OMICS_01555 | SCR_003215 | NHGRI Talking Glossary, NHGRI Talking Glossary of Genetic Terms | 2026-08-05 10:43:47 | 0 | ||||||
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Database of Interacting Proteins (DIP) Resource Report Resource Website 100+ mentions |
Database of Interacting Proteins (DIP) (RRID:SCR_003167) | DIP | data or information resource, data repository, storage service resource, database, data analysis service, production service resource, service resource, analysis service resource | Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available. | blast, cellular network, ligand-receptor complex, ligand, network, protein, protein interaction, protein ligand, protein-protein interaction, protein receptor, receptor, sequence, interaction, regulatory pathway, signaling pathway, protein binding, bio.tools, FASEB list |
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: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: IMEx - The International Molecular Exchange Consortium is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: NIH Data Sharing Repositories is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of California at Los Angeles; California; USA |
NIGMS | PMID:14681454 | Free, Available for download, Freely available | OMICS_01905, nif-0000-00569, r3d100010882, biotools:dip | https://dip.doe-mbi.ucla.edu/dip/Main.cgi, https://bio.tools/dip, https://doi.org/10.17616/R3431F | SCR_003167 | , Database of Interacting Proteins, DIP, Database of Interacting Proteins (DIP) | 2026-08-05 10:43:47 | 153 | ||||
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Piano Resource Report Resource Website 100+ mentions |
Piano (RRID:SCR_003200) | software resource, data processing software, software application, data analysis software | Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses. | r, omics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chalmers University of Technology; Gothenburg; Sweden has parent organization: Bioconductor |
PMID:23444143 | Free, Available for download, Freely available | OMICS_01558, biotools:piano | https://bio.tools/piano | SCR_003200 | 2026-08-05 10:43:47 | 182 | |||||||
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Solas Resource Report Resource Website 1+ mentions |
Solas (RRID:SCR_003168) | data processing software, source code, software application, data analysis software, sequence analysis software, software resource | Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample. | r statistical package, rna seq, exon prediction, exon splicing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
Free, Available for download, Freely available | biotools:solas, OMICS_01339 | https://bio.tools/solas | SCR_003168 | 2026-08-05 10:43:47 | 8 | ||||||||
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DIALIGN Resource Report Resource Website 10+ mentions |
DIALIGN (RRID:SCR_003041) | DIALIGN | web service, data access protocol, software resource, data analysis service, production service resource, service resource, analysis service resource | Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/ | dna, protein, sequence alignment, sequence, alignment, fasta, genome, genomic sequence, homology, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15215344 PMID:23620293 DOI:10.1186/1748-7188-3-6 |
Free, Available for download, Freely available | nif-0000-30417, OMICS_24606, OMICS_00973, biotools:dialign-tx | http://dialign.gobics.de/, https://bio.tools/dialign-tx | https://sources.debian.org/src/dialign-tx/ | SCR_003041 | DIALIGN at GOBICS | 2026-08-05 10:43:45 | 43 | ||||
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rDiff Resource Report Resource Website 1+ mentions |
rDiff (RRID:SCR_003162) | data processing software, software application, sequence analysis software, data analysis software, software resource | Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples. | differential rna processing, rna processing, rna seq | is listed by: OMICtools | PMID:23585274 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01338 | SCR_003162 | 2026-08-05 10:43:47 | 6 | ||||||||
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PIRSF Resource Report Resource Website 10+ mentions |
PIRSF (RRID:SCR_003352) | PIRSF | data or information resource, standard specification, narrative resource, database | A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF. | protein annotation, classification, protein, superfamily, functional site, protein name, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: UniProtKB has parent organization: Protein Information Resource |
NHGRI U01-HG02712; NSF DBI-0138188; NSF ITR-0205470 |
PMID:19455212 PMID:14681371 |
Free, Freely available | biotools:pirsf, nif-0000-03294, OMICS_01697 | https://bio.tools/pirsf | http://pir.georgetown.edu/pirsf/ | SCR_003352 | PIR SuperFamily, Protein Information Resource SuperFamily | 2026-08-05 10:43:49 | 28 |
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