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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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VariantMaster Resource Report Resource Website |
VariantMaster (RRID:SCR_000569) | VariantMaster | software resource | Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores. | unix/linux, clinical, genetics, high throughput sequencing, monogenic disease, variant, snp, indel |
is listed by: OMICtools has parent organization: SourceForge |
Genetic disease, Tumor | PMID:24389049 | Free, Available for download, Freely available, | OMICS_02261 | SCR_000569 | SciCrunch Registry | VariantMaster - Extract causative variants for monogenic and sporadic genetic diseases | 2026-10-10 12:35:41 | 0 | |||||
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OnEx - Ontology Evolution Explorer Resource Report Resource Website 1+ mentions |
OnEx - Ontology Evolution Explorer (RRID:SCR_000602) | OnEx | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released | ontology, gene, protein, function, process, component, ontology or annotation browser, evolution, trend, annotation, version |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: NCI Thesaurus is related to: OBO has parent organization: University of Leipzig; Saxony; Germany |
BMBF 01AK803E; DFG |
PMID:19678926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02273, nlx_149129 | http://www.izbi.de/onex, http://aprilia.izbi.uni-leipzig.de:8080/onex/ | SCR_000602 | SciCrunch Registry | Ontology Evolution Explorer (OnEx), Ontology Evolution Explorer | 2026-10-10 12:35:42 | 1 | ||||
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CorQ Resource Report Resource Website 1+ mentions |
CorQ (RRID:SCR_000660) | software resource | A set of perl programs that correct errors in 454 pyrosequences by identifying and flagging poor quality insertions, deletions and substitutions within an alignment. The algorithm utilizes the inherent base quality in sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors. | homopolymer, indel, corq, uneven read mapping, pyrosequence error, forward errors |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
PMID:24039850 | OMICS_01039 | SCR_000660 | SciCrunch Registry | 2026-10-10 12:35:43 | 1 | |||||||||
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Biometric Research Branch: ArrayTools Resource Report Resource Website 1+ mentions |
Biometric Research Branch: ArrayTools (RRID:SCR_000778) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in. | visualization, statistic, analysis, dna, microarray, gene, expression, c, java, excel |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30199 | SCR_000778 | SciCrunch Registry | BRB ArrayTools | 2026-10-10 12:35:40 | 6 | ||||||||
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GenomeWeb Resource Report Resource Website 1+ mentions |
GenomeWeb (RRID:SCR_000650) | GenomeWeb | blog, data or information resource, job resource, narrative resource, video resource | An independent, privately-held online and print publisher based in New York that serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. GenomeWeb's editorial mission is to serve readers with exclusive, in-depth coverage of the technology, institutions, and scientists that make up the worldwide research enterprise of molecular biology. We operate the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics. Our expert editors report and write with precision and clarity. GenomeWeb users can be found in major scientific organizations around the world, including biopharmaceutical companies, important research universities, biomedical institutes, and government laboratories. Our advertisers include leading suppliers of research tools, analytical instruments, and information technology. Getting started is easy - just register, and use your workplace e-mail address to maximize your access to content. Once you're logged in, you'll have complete free access to GenomeWeb Daily News, The Daily Scan, all of Genome Technology magazine, every GenomeWeb blog, and much more. GenomeWeb Free Content * GenomeWeb Daily News offers breaking news as well as feature articles on genomics, proteomics, bioinformatics, and more. Daily News covers not only the science and business news, but also regulatory and policy updates. Published online and twice daily by e-mail bulletin. * The Daily Scan is a roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin. * Genome Technology: GenomeWeb's magazine covers news, trends, people, and technologies in the systems biology field. It also includes Tech Guides, which feature expert troubleshooting advice on specific lab challenges, and Research Trend Digests. Published 10 times per year. Subscriptions to the print edition are free to active researchers in the US and $29 per year for non-scientists or anyone outside the US. Non-US researchers are eligible for a free subscription to the digital edition of Genome Technology. We may contact subscribers from time to time to requalify for the magazine, in compliance with our third-party readership audit. * Careers: Our Careers page includes content to help scientists in their jobs, with links to relevant external blog posts, profiles of alternative job paths, and more. Careers also includes our Job Listings board, where anyone can post job ads for free. * Cancer Minute: Updated daily and published by e-mail bulletin weekly, Cancer Minute rounds up the latest oncology peer-reviewed literature as well as news and blog posts. * Informatics Iron: This blog covers high-performance computing and the hardware side of bioinformatics, from GPUs to compute clusters and more. * The Sample: This blog focuses on a range of topics of interest to clinical labs, including the adoption of molecular tools, issues related to lab management, in-depth coverage of the major reference labs, and more. GenomeWeb Premium Content All GenomeWeb premium content provides readers with in-depth, exclusive coverage in key technology or application areas. These publications include business, technology, and research news; patent and IP information; product launches and upgrades; and hirings, promotions, and other people news. | genomics, proteomics, bioinformatics, biomedical, biopharmaceutical, genomic, molecular biology, research, rnai, scientist, technology, array, mdx, informatics, pcr, mirna, sequencing |
is used by: OncoTrack is listed by: OMICtools is parent organization of: Daily Scan |
OMICS_01731, nif-0000-10238 | SCR_000650 | SciCrunch Registry | GenomeWeb LLC | 2026-10-10 12:35:39 | 2 | ||||||||
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GEUVADIS Resource Report Resource Website 1+ mentions |
GEUVADIS (RRID:SCR_000684) | GEUVADIS | consortium, data or information resource, organization portal, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genetic, variation, health, disease, medical, sequencing, high-throughput sequencing, human genome, genome, genomics, personalized medicine, genomic medicine | is listed by: OMICtools | European Union ; FP7 ; HEALTH |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01779, SCR_013706 | SCR_000684 | SciCrunch Registry | Genetic European Variation in Health and Disease - A European Medical Sequencing Consortium, GEUVADIS Consortium, Genetic European Variation in Health and Disease | 2026-10-10 12:35:39 | 1 | ||||||
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DeNovoGear Resource Report Resource Website 1+ mentions |
DeNovoGear (RRID:SCR_000670) | software resource | A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations. | de novo, mutation, sequence, dna, rna, error modeling, exome analysis |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:23975140 | Free, Available for download, Freely available | OMICS_00083 | https://github.com/denovogear/denovogear | SCR_000670 | SciCrunch Registry | 2026-10-10 12:35:40 | 3 | |||||||
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SRMA Resource Report Resource Website |
SRMA (RRID:SCR_000669) | SRMA | software resource | A post-alignment micro re-aligner for next-generation high throughput sequencing data. | matlab, sequence re-alignment, command-line, java, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20932289 | Free, Available for download, Freely available | biotools:srma, OMICS_01079 | https://bio.tools/srma | SCR_000669 | SciCrunch Registry | Short Read Micro re-Aligner | 2026-10-10 12:35:39 | 0 | |||||
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KLEIO Resource Report Resource Website 1+ mentions |
KLEIO (RRID:SCR_000698) | KLEIO | service resource | An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008 | semantic search, entity recognition |
is listed by: FORCE11 is listed by: OMICtools is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | Acknowledgement required, See Terms of Use | OMICS_01186, nlx_44954 | http://www.nactem.ac.uk/software/kleio/ | SCR_000698 | SciCrunch Registry | 2026-10-10 12:35:40 | 3 | ||||||
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FineSplice Resource Report Resource Website 1+ mentions |
FineSplice (RRID:SCR_000691) | software resource | A software pipeline based on TopHat2 combined with a splice junction detection algorithm. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24574529 | Free, Available for download, Freely available | OMICS_03274 | SCR_000691 | SciCrunch Registry | 2026-10-10 12:35:39 | 1 | ||||||||
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BISMA Resource Report Resource Website 10+ mentions |
BISMA (RRID:SCR_000688) | software resource, web application | An online tool for the analysis of bisulfite sequencing DNA methylation data. The software has specificity and quality control functions that allow the user to compile a set of sequences. | bisulfite sequencing, dna methylation, quality control |
is listed by: OMICtools has parent organization: Jacobs University Bremen; Bremen; Germany |
PMID:20459626 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00592 | SCR_000688 | SciCrunch Registry | Bisulfite Sequencing DNA Methylation Analysis, BISMA: Analysis of primary bisulfite sequencing data manual | 2026-10-10 12:35:45 | 13 | |||||||
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jmzIdentML API Resource Report Resource Website |
jmzIdentML API (RRID:SCR_000878) | software resource | A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. | standalone software, mac os x, unix/linux, windows, java |
is listed by: OMICtools has parent organization: Google Code |
PMID:22539429 | Free, Available for download, Freely available | OMICS_03339 | SCR_000878 | SciCrunch Registry | 2026-10-10 12:35:42 | 0 | ||||||||
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SciRoKo Resource Report Resource Website 1+ mentions |
SciRoKo (RRID:SCR_000941) | software resource | Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output. | genomics, comparative, genome, microsatellite, analysis, investigation | is listed by: OMICtools | PMID:17463017 | Free, Available for download, Freely available | OMICS_00113 | SCR_000941 | SciCrunch Registry | 2026-10-10 12:35:42 | 6 | ||||||||
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CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | SciCrunch Registry | 2026-10-10 12:35:49 | 19 | |||||||
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GraphIBD Resource Report Resource Website |
GraphIBD (RRID:SCR_001174) | software resource | Identity-by-descent (IBD) association testing software for genome-wide association study analysis. It requires an IBD detection method such as Beagle FastIBD to run first. GraphIBD then builds upon the IBD information to test if the IBD segments show association to the traits. | identity-by-descent, genome-wide association study |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
NHLBI K25-HL080079 | PMID:24158599 | Free, Available for download, Freely available | OMICS_02183 | SCR_001174 | SciCrunch Registry | 2026-10-10 12:35:54 | 0 | |||||||
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EMI Resource Report Resource Website |
EMI (RRID:SCR_001171) | EMI | software resource | Clustering software which uses pairwise identity-by-descent (IBD) segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome. | clustering, identity-by-descent |
is listed by: OMICtools has parent organization: Aarhus University; Aarhus; Denmark |
PMID:24363374 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02186 | SCR_001171 | SciCrunch Registry | Efficient Multiple-IBD | 2026-10-10 12:35:55 | 0 | ||||||
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Shimmer Resource Report Resource Website |
Shimmer (RRID:SCR_001164) | software resource | Software package that detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. It uses Fisher's exact test along with multiple testing correction (Benjamini-Hochberg) to find significant differences between allele composition with a specified false discovery rate. | standalone software, bam |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
PMID:23620360 | Free, Available for download, Freely available | OMICS_03612 | SCR_001164 | SciCrunch Registry | 2026-10-10 12:35:48 | 0 | ||||||||
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DiMO Resource Report Resource Website 1+ mentions |
DiMO (RRID:SCR_001168) | DiMO | software resource | Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. | r, motif, perceptron |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:24369152 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02190 | SCR_001168 | SciCrunch Registry | Discriminative Motif Optimizer, DiMO: Discriminative Motif Optimizer | 2026-10-10 12:35:47 | 1 | ||||||
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ExomePeak Resource Report Resource Website 1+ mentions |
ExomePeak (RRID:SCR_001076) | exomePeak | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. | r, matlab |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Texas at San Antonio; Texas; USA |
PMID:23589649 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00570 | SCR_001076 | SciCrunch Registry | 2026-10-10 12:35:45 | 5 | |||||||
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Starr Resource Report Resource Website |
Starr (RRID:SCR_001071) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences. | data import, quality, visualization, r, genomics, mapping, data analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20398407 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00811 | SCR_001071 | SciCrunch Registry | 2026-10-10 12:35:45 | 0 |
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