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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | Free, Freely available, Available for download | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | hot_scan | 2026-09-05 06:24:54 | 6 | ||||||
|
rDock Resource Report Resource Website 100+ mentions |
rDock (RRID:SCR_002838) | software resource | A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24722481 | Free, Freely available, Available for download | OMICS_03835 | SCR_002838 | 2026-09-05 06:24:54 | 122 | ||||||||
|
Basic4Cseq Resource Report Resource Website 1+ mentions |
Basic4Cseq (RRID:SCR_002836) | software resource | An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile. | software package, unix/linux, mac os x, windows, r, quality control, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:25078398 | Free, Freely available, Available for download | OMICS_05202 | SCR_002836 | Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data | 2026-09-05 06:24:54 | 6 | |||||||
|
SMRT-Analysis Resource Report Resource Website 100+ mentions |
SMRT-Analysis (RRID:SCR_002942) | software resource | Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences. | software suite |
is listed by: OMICtools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05142 | http://www.pacb.com/devnet/, https://sources.debian.org/src/smrtanalysis/ | SCR_002942 | SMRT Analysis | 2026-09-05 06:24:55 | 148 | |||||||
|
mzR Resource Report Resource Website 1+ mentions |
mzR (RRID:SCR_002856) | software resource | Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | standalone software, mac os x, unix/linux, windows, r, data import, infrastructure, mass spectrometry, metabolomics, proteomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02654 | SCR_002856 | mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files | 2026-09-05 06:24:54 | 1 | ||||||||
|
BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-09-05 06:24:54 | 0 | |||||||
|
PAPi Resource Report Resource Website 50+ mentions |
PAPi (RRID:SCR_002857) | software resource | An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20929912 | Free, Freely available, Available for download | OMICS_02653 | SCR_002857 | PAPi - Predict metabolic pathway activity based on metabolomics data, Pathway Activity Profiling | 2026-09-05 06:24:54 | 56 | |||||||
|
ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | catalog, data or information resource, data repository, database, service resource, storage service resource | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Commission ; European Union ; Gen2Phen 200754; NHGRI P41 HG003619; SLING 226073 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae, https://doi.org/10.17616/R3302G | SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-09-05 06:24:56 | 7814 | ||||
|
CNVassoc Resource Report Resource Website 1+ mentions |
CNVassoc (RRID:SCR_002901) | software resource | Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21609482 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02609 | SCR_002901 | CNVassoc: Association analysis of CNV data | 2026-09-05 06:24:55 | 1 | |||||||
|
SURPI Resource Report Resource Website 10+ mentions |
SURPI (RRID:SCR_003071) | SURPI | software resource | Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples. | pipeline, cloud based pipeline, pathogen identification |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
PMID:24899342 | OMICS_04623 | https://github.com/chiulab/surpi | SCR_003071 | Sequence-based Ultra-Rapid Pathogen Identification | 2026-09-05 06:24:57 | 13 | ||||||
|
MethDB Resource Report Resource Website 10+ mentions |
MethDB (RRID:SCR_003108) | MethDB | data or information resource, data repository, database, service resource, storage 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 | 2026-09-05 06:24:58 | 15 | |||||
|
FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-09-05 06:24:57 | 0 | ||||||
|
DnaSP Resource Report Resource Website 5000+ mentions |
DnaSP (RRID:SCR_003067) | DnaSP | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:24:57 | 6215 | |||||
|
JuncBASE Resource Report Resource Website 10+ mentions |
JuncBASE (RRID:SCR_003103) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:24:58 | 19 | ||||||||
|
pFind Resource Report Resource Website 100+ mentions |
pFind (RRID:SCR_003011) | software resource | A search engine system for automated peptide and protein identification from tandem mass spectra. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:17702057 | OMICS_02467 | SCR_003011 | 2026-09-05 06:24:56 | 132 | |||||||||
|
JETTA Resource Report Resource Website 1+ mentions |
JETTA (RRID:SCR_003091) | JETTA | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:24:57 | 3 | |||||||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | 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 | 2026-09-05 06:24:57 | 1860 | ||||
|
tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-09-05 06:24:57 | 4 | ||||||
|
R-pbh5 Resource Report Resource Website |
R-pbh5 (RRID:SCR_003026) | software library, software resource, software toolkit | Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5. | software package, r | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_05139 | https://github.com/extemporaneousb/R-pbh5 | SCR_003026 | 2026-09-05 06:24:56 | 0 | ||||||||
|
Isopat Resource Report Resource Website |
Isopat (RRID:SCR_003025) | software resource | Software function that calculates the isotopic pattern (fine structures) for a given chemical formula. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_02409 | https://isopat.sourceforge.net/ | SCR_003025 | isopat: Calculation of isotopic pattern for a given molecular formula | 2026-09-05 06:24:56 | 0 |
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