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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CTCFBSDB Resource Report Resource Website 50+ mentions |
CTCFBSDB (RRID:SCR_002279) | CTCFBSDB, CTCFBSDB 2.0 | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource |
A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search. |
cctc-binding factor, ctcf, ctcf binding site, insulator, genomic insulator, genome, binding site, FASEB list |
is listed by: OMICtools has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PMID:23193294 PMID:17981843 |
nif-0000-02703, OMICS_00530 | http://insulatordb.utmem.edu/ | SCR_002279 | CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators, CTCFBSDB 2.0: A database for CTCF binding sites and genome organization | 2026-09-12 12:55:39 | 69 | ||||||
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FR-HIT Resource Report Resource Website 10+ mentions |
FR-HIT (RRID:SCR_002181) | FR-HIT | software resource | An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit. | metagenomics, bioinformatics, sequence analysis, next-generation sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Freely available | OMICS_01850 | SCR_002181 | FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance, Metagenome Fragment Recruitment at High Identity with Tolerance, Fragment Recruitment at High Identity with Tolerance | 2026-09-12 12:55:37 | 11 | |||||||
|
flowPlots Resource Report Resource Website |
flowPlots (RRID:SCR_002177) | software resource | Software for analysis plots and data class for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, data representation, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05608 | SCR_002177 | flowPlots: analysis plots and data class for gated flow cytometry data | 2026-09-12 12:55:37 | 0 | ||||||||
|
metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | metaRNASeq: Meta-analysis of RNA-seq data | 2026-09-12 12:55:37 | 35 | |||||||
|
DEMI Resource Report Resource Website 1+ mentions |
DEMI (RRID:SCR_002291) | software resource | R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes. | standalone software, affymetrix, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24586062 | Free, Available for download, Freely available, Acknowledgement requested | OMICS_03438 | http://cran.r-project.org/web/packages/demi/ | SCR_002291 | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-09-12 12:55:39 | 6 | ||||||
|
flowCore Resource Report Resource Website 100+ mentions |
flowCore (RRID:SCR_002205) | software resource | A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is used by: flowBeads is listed by: OMICtools has parent organization: Bioconductor |
PMID:19358741 | Artistic License, v2 | OMICS_05596 | SCR_002205 | flowCore: Basic structures for flow cytometry data | 2026-09-12 12:55:38 | 376 | |||||||
|
Cancer Genomics Consortium Resource Report Resource Website 1+ mentions |
Cancer Genomics Consortium (RRID:SCR_002384) | CGC | community building portal, data or information resource, organization portal, portal | Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization. | cytogenetics, molecular genetics, molecular pathology, microarray technology, cancer diagnosis, cancer research, microarry, cytogenomics, cancer cytogenomics, cancer genetics, genetics | is listed by: OMICtools | Cancer | Membership fee, Account required | OMICS_01776 | SCR_002384 | CCMC, Cancer Cytogenomics Microarray Consortium | 2026-09-12 12:55:40 | 6 | ||||||
|
Clinical and Laboratory Standards Institute Resource Report Resource Website 100+ mentions |
Clinical and Laboratory Standards Institute (RRID:SCR_002382) | CLSI | data or information resource, knowledge environment, narrative resource, standard specification | A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world. | clinical, laboratory testing, quality, clinical laboratory testing standard, laboratory, testing | is listed by: OMICtools | Membership fee | OMICS_01777 | SCR_002382 | 2026-09-12 12:55:40 | 195 | ||||||||
|
Quick-R Resource Report Resource Website 1+ mentions |
Quick-R (RRID:SCR_002417) | Quick-R | book, data or information resource, narrative resource, training material | Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it. | r, programming language, code | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01760 | SCR_002417 | Quick-R - accessing the power of R | 2026-09-12 12:55:40 | 5 | |||||||
|
realSFS Resource Report Resource Website 10+ mentions |
realSFS (RRID:SCR_002493) | data analysis software, data processing software, software application, software resource | Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | allele frequency estimation, snp calling | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00071 | SCR_002493 | 2026-09-12 12:55:41 | 27 | |||||||||
|
flowBeads Resource Report Resource Website |
flowBeads (RRID:SCR_002440) | software resource | Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
uses: flowCore is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available | OMICS_05592 | SCR_002440 | flowBeads: Analysis of flow bead data | 2026-09-12 12:55:41 | 0 | ||||||||
|
flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-09-12 12:55:39 | 7 | ||||||||
|
R Tutorial - An R Introduction to Statistics Resource Report Resource Website 10+ mentions |
R Tutorial - An R Introduction to Statistics (RRID:SCR_002394) | R Tutorial | book, data or information resource, narrative resource, training material | Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available. | r, statistics, gpu computing | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_01762 | SCR_002394 | R Tutorial (An R Introduction to Statistics) | 2026-09-12 12:55:40 | 23 | |||||||
|
DWGSIM Resource Report Resource Website 50+ mentions |
DWGSIM (RRID:SCR_002342) | DWGSIM | software resource | Whole Genome Simulator for Next-Generation Sequencing. | next-generation sequencing, whole genome simulation |
is listed by: OMICtools is listed by: Debian |
GNU General Public License, v2 | OMICS_00249 | https://sources.debian.org/src/dwgsim/ | SCR_002342 | 2026-09-12 12:55:40 | 53 | |||||||
|
BEETL-fastq Resource Report Resource Website |
BEETL-fastq (RRID:SCR_002341) | software resource | Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads. | Searchable compressed archive, DNA reads, compresses FASTQ-formatted DNA reads, bio.tools, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Burrows-Wheeler transform |
PMID:24950811 | Free, Available for download, Freely available | OMICS_04900, biotools:beetl | https://bio.tools/beetl | SCR_002341 | 2026-09-12 12:55:40 | 0 | |||||||
|
RepARK Resource Report Resource Website 1+ mentions |
RepARK (RRID:SCR_002333) | software resource | Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome. | standalone software | is listed by: OMICtools | PMID:24634442 | OMICS_03446 | SCR_002333 | Repetitive motif detection by Assembly of Repetitive K-mers | 2026-09-12 12:55:39 | 7 | ||||||||
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Variant Reporter Software Resource Report Resource Website 50+ mentions |
Variant Reporter Software (RRID:SCR_002329) | data analysis software, data processing software, sequence analysis software, software application, software resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017. Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation. |
comparative sequencing, mutation detection, snp discovery, sequence confirmation |
is listed by: OMICtools is listed by: Thermo Fisher Scientific has parent organization: Life Technologies |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01818 | http://www.lifetechnologies.com/order/catalog/product/4385261 | SCR_002329 | 2026-09-12 12:55:39 | 85 | ||||||||
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DNA DataBank of Japan (DDBJ) Resource Report Resource Website 500+ mentions |
DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) | DDBJ | data or information resource, data repository, database, service resource, storage service resource | Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases. | nucleotide sequence, genome, dna, dna database, dna research, nucleotide, phylogenetics, protein, sequence, protein binding, gene expression, gene, genetics, nucleoid, genomics, protein binding, gold standard, 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: Debian is listed by: bio.tools is related to: INSDC is related to: GenBank is related to: INSDC is related to: European Nucleotide Archive (ENA) is related to: GenBank is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: PDBe - Protein Data Bank in Europe is related to: PDBe - Protein Data Bank in Europe is related to: European Nucleotide Archive (ENA) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: NCBI Assembly Archive Viewer has parent organization: National Institute of Genetics; Shizuoka; Japan is parent organization of: DDBJ Omics Archive is parent organization of: BodyMap-Xs is parent organization of: DDBJ Sequence Read Archive is parent organization of: CIBEX: Center for Information Biology gene EXpression database is parent organization of: Japanese Genotype-phenotype Archive (JGA) |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:26578571 PMID:25477381 |
Free, Freely available, | OMICS_01644, biotools:ddbj, nif-0000-02740, r3d100010218 | https://bio.tools/ddbj, https://doi.org/10.17616/R3M01R | SCR_002359 | DNA DataBank of Japan (DDBJ), DNA DataBank of Japan, DDBJ, DNA Data Bank of Japan, DDBJ - DNA Data Bank of Japan | 2026-09-12 12:55:40 | 709 | ||||
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Mason Resource Report Resource Website 100+ mentions |
Mason (RRID:SCR_002476) | simulation software, software application, software resource | Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads. | read simulating software, sequencing simulation, haplotype simulation | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00252 | SCR_002476 | Mason2 | 2026-09-12 12:55:41 | 169 | ||||||||
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ShotGun Resource Report Resource Website 10+ mentions |
ShotGun (RRID:SCR_002529) | data analysis software, data processing software, sequence analysis software, simulation software, software application, software resource | Software for short read simulating in order to facilitate sequencing-based study designs. | sequence based study design, short read stimulation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:23357921 | Free, Available for download, Freely available | biotools:abcd, OMICS_00255 | https://bio.tools/abcd | SCR_002529 | ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs | 2026-09-12 12:55:42 | 35 |
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