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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Kansas State University; Kansas; USA Resource Report Resource Website 1+ mentions |
Kansas State University; Kansas; USA (RRID:SCR_001533) | KSU | university | Public doctoral university located in Manhattan, Kansas that is involved with research, especially agricultural. | public, doctoral, university, research, agriculture, degree |
is parent organization of: BeetleBase is parent organization of: QGene is parent organization of: Basic Research Immersion Training Experience Veterinary Student Program is parent organization of: KSU AFM Imaging Group is parent organization of: Kansas State University Labs and Facilities is parent organization of: Kansas State University - INBRE Bioinformatics Core Facility |
Free, Freely available | Wikidata:Q31249, nlx_62700, ISNI:0000 0001 0737 1259, grid.36567.31, Crossref funder ID:100007765 | https://ror.org/05p1j8758 | SCR_001533 | Kansas State University | 2026-02-07 02:05:39 | 2 | ||||||
|
Enriched Domain Detector Resource Report Resource Website 1+ mentions |
Enriched Domain Detector (RRID:SCR_001693) | EDD | software resource | A ChIP-seq peak caller for detection of megabase domains of enrichment. | standalone software, unix/linux, mac os x | is listed by: OMICtools | PMID:24782521 | Free, Available for download, Freely available | OMICS_03964 | SCR_001693 | EDD - Enriched Domain Detector | 2026-02-07 02:05:42 | 7 | ||||||
|
IDRISI Resource Report Resource Website 10+ mentions |
IDRISI (RRID:SCR_001696) | IDRISI | software resource | Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more. | gis, geospatial, monitor, model, earth system, earth, image processing, surface analysis, vertical application, land change analysis, earth trend |
is listed by: CINERGI has parent organization: Clark University; Massachusetts; USA |
Free, Freely Available | SCR_001696 | IDRISI Selva | 2026-02-07 02:05:34 | 37 | ||||||||
|
CNVrd2 Resource Report Resource Website 1+ mentions |
CNVrd2 (RRID:SCR_001723) | software resource | A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions. | standalone software, illumina, unix/linux, mac os x, windows, r, clustering., copy number variation, coverage, linkage disequilibrium, snp, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23646200 | Free, Available for download, Freely available | OMICS_03924 | http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html https://github.com/hoangtn/CNVrd2 |
SCR_001723 | CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data | 2026-02-07 02:05:42 | 5 | ||||||
|
sSeq Resource Report Resource Website 10+ mentions |
sSeq (RRID:SCR_001719) | sSeq | software resource | Software package to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution. | rna-seq, differential expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23589650 | Free, Available for download, Freely available | OMICS_01962 | SCR_001719 | sSeq - Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size | 2026-02-07 02:05:34 | 46 | ||||||
|
King's College London; London; United Kingdom Resource Report Resource Website 1+ mentions |
King's College London; London; United Kingdom (RRID:SCR_001744) | KCL | university | Public research university located in London, United Kingdom that offers undergraduate, graduate, and professional degree programs in medicine, economics, social sciences, etc. | public, research, london, medical school, undergraduate, graduate |
uses: ReadCube is related to: AddNeuroMed is related to: EU-AIMS is related to: NEWMEDS is related to: ONE Study is related to: EMIF is parent organization of: Pliny is parent organization of: TRANSFoRm is parent organization of: Kings College London Infectious Diseases BioBank is parent organization of: Major depressive disorder neuroimaging database is parent organization of: Bipolar Disorder Neuroimaging Database is parent organization of: Marker And Gene Interpolation and Correlation is parent organization of: Brain Segmentation Testing Protocol is parent organization of: MSbind is parent organization of: Pharmacological Imaging and Pattern Recognition toolbox is parent organization of: Neuromuscular disease outcome measures is parent organization of: Haemophilia B Mutation Database is parent organization of: Brain and Body Genetic Resource Exchange is parent organization of: LIGand Attachment SITE Database is parent organization of: Rodent Brain Extraction Tool is parent organization of: AddNeuroMed is parent organization of: NEWMEDS is parent organization of: MRC London Neurodegenerative Diseases Brain Bank is parent organization of: Kings College London Microscopy Innovation Centre Core Facility |
Free, Freely Available | grid.13097.3c, nlx_60659, Crossref funder ID:100009360, ISNI:0000 0001 2322 6764, Wikidata:Q245247 | https://ror.org/0220mzb33 | SCR_001744 | King's College | 2026-02-07 02:05:42 | 1 | ||||||
|
pairedBayes Resource Report Resource Website 1+ mentions |
pairedBayes (RRID:SCR_001738) | pairedBayes | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments. | r, rna-seq |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_01958 | SCR_001738 | 2026-02-07 02:05:35 | 1 | ||||||||
|
DNACLUST Resource Report Resource Website 1+ mentions |
DNACLUST (RRID:SCR_001771) | software resource | Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads. | cluster, dna sequence, gene, 16s rrna pyrosequencing read, microbiome |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian has parent organization: SourceForge |
PMID:21718538 DOI:10.1186/1471-2105-12-271 |
Free, Available for download, Freely available | OMICS_01955 | https://sources.debian.org/src/dnaclust/ | SCR_001771 | DNAClust | 2026-02-07 02:05:36 | 9 | ||||||
|
InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | Free, Freely available | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine https://bio.tools/intermine |
http://intermine.github.io/intermine.org/ | SCR_001772 | 2026-02-07 02:05:43 | 21 | |||||
|
ATCC Resource Report Resource Website 10000+ mentions |
ATCC (RRID:SCR_001672) | ATCC | commercial organization | Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities. | biomaterial, cell line, culture, microorganism, proteomics, protozoa, tissue, bacteria, virus, fungus, standardization, molecular genomics, reagent, yeast, microbial culture, stem cell, dna, FASEB list |
is used by: NIA Mouse cDNA Project Home Page is used by: NIF Data Federation is listed by: One Mind Biospecimen Bank Listing is related to: Cell Line Knowledge Base is related to: Vector Database is related to: Hyper Cell Line Database is related to: BEI Resource Repository is related to: NCBI BioSample is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: Integrated Cell Lines is related to: ATCC STR database is parent organization of: Mantle Cell Lymphoma Cell Bank works with: Cellosaurus |
Free, Freely Available | ISNI: 0000 0001 2161 7948, Wikidata: Q2843042, grid.281196.5, nif-0000-10159 | https://ror.org/03thhhv76 | SCR_001672 | ATCC: The Global Bioresource Center, American Type Culture Collection, ATCC(dna), ATCC(in host) | 2026-02-07 02:05:41 | 106375 | ||||||
|
RSVSim Resource Report Resource Website 10+ mentions |
RSVSim (RRID:SCR_001777) | software resource | A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates. | unix/linux, mac os x, windows, r, sequencing, structural variation |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23620362 | Free, Available for download, Freely available | OMICS_03822 | SCR_001777 | RSVSim: an R/Bioconductor package for the simulation of structural variations | 2026-02-07 02:05:43 | 16 | |||||||
|
Annual Reviews: A Nonprofit Scientific Publisher Resource Report Resource Website 10+ mentions |
Annual Reviews: A Nonprofit Scientific Publisher (RRID:SCR_001655) | journal article | Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields. | biomedical, life science, literature, physical science, review, social science | Free, Freely Available | nif-0000-10150 | SCR_001655 | Annual Reviews | 2026-02-07 02:05:41 | 26 | |||||||||
|
TCC Resource Report Resource Website 1+ mentions |
TCC (RRID:SCR_001779) | TCC | software resource | An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq). | rna-seq, differential expression, high throughput sequencing |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23837715 | Free, Available for download, Freely available | OMICS_01952 | SCR_001779 | Tag Count Comparison, TCC: Differential expression analysis for tag count data with robust normalization strategies | 2026-02-07 02:05:35 | 8 | ||||||
|
CCAT Resource Report Resource Website 50+ mentions |
CCAT (RRID:SCR_001843) | CCAT | software resource | THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:20371496 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00428, biotools:ccat | https://bio.tools/ccat | SCR_001843 | Control based ChIP-Seq Analysis Tools | 2026-02-07 02:05:45 | 76 | |||||
|
ExpressionPlot Resource Report Resource Website 1+ mentions |
ExpressionPlot (RRID:SCR_001904) | expressionplot | software resource | Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. | analysis, rna-seq, microarray, gene expression, affymetrix, prototype | is listed by: OMICtools | PMID:21797991 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01939 | SCR_001904 | 2026-02-07 02:05:37 | 9 | |||||||
|
S-MART Resource Report Resource Website 10+ mentions |
S-MART (RRID:SCR_001908) | S-MART | software resource | Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries. | high throughput sequencing, rna-seq, chip-seq, python, linux, ms windows, mac, short-read, selection, visualization, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21998740 | Free, Available for download, Freely available | OMICS_01937, biotools:mapperanalyzer, biotools:s-mart | https://bio.tools/s-mart https://bio.tools/mapperanalyzer |
SCR_001908 | 2026-02-07 02:05:37 | 23 | ||||||
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Korea Advanced Institute of Science and Technology; Daejeon; South Korea Resource Report Resource Website 1+ mentions |
Korea Advanced Institute of Science and Technology; Daejeon; South Korea (RRID:SCR_001902) | KAIST | institution | Institute dedicated to research in science and technology in South Korea modeled after a research university. | south korea, research, science, technology |
is parent organization of: NIRS-SPM is parent organization of: FiGS |
Available to the research community | grid.37172.30, ISNI: 0000 0001 2292 0500, Crossref funder ID: 501100007107, Wikidata: Q39949, nlx_155859 | https://ror.org/05apxxy63 | http://www.kaist.edu/english/ | SCR_001902 | Korea Advanced Institute of Science and Technology | 2026-02-07 02:05:38 | 1 | |||||
|
THetA Resource Report Resource Website 100+ mentions |
THetA (RRID:SCR_001860) | software resource | An algorithm that estimates the tumor purity and clonal / subclonal copy number aberrations directly from high-throughput DNA sequencing data. | standalone software |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
PMID:23895164 | Free, Available for download, Freely available | OMICS_03562 | http://compbio.cs.brown.edu/projects/theta/ | SCR_001860 | THetA: Tumor Heterogeneity Analysis, Tumor Heterogeneity Analysis, Tumor Heterogeneity Analysis (THetA) | 2026-02-07 02:05:45 | 203 | ||||||
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University of Alberta; Alberta; Canada Resource Report Resource Website 1+ mentions |
University of Alberta; Alberta; Canada (RRID:SCR_001853) | university | Public research university in Edmonton, Alberta, Canada that offers degree programs in a variety of fields including business, arts, education, engineering, nursing, and medicine. | public, research, university, alberta, canada |
is related to: Alberta Diabetes Institute IsletCore database is parent organization of: T3DB is parent organization of: DrugBank is parent organization of: Arthur Prochazka Laboratory, University of Alberta is parent organization of: Proteome Analyst Specialized Subcellular Localization Server is parent organization of: Canadian Biosample Repository is parent organization of: Blood Borne Pathogens Laboratory is parent organization of: Small Molecule Pathway Database is parent organization of: NGS-SNP is parent organization of: PHAge Search Tool is parent organization of: PolySearch is parent organization of: YMDB - Yeast Metabolome Database is parent organization of: BacMap: Bacterial Genome Atlas is parent organization of: HMDB is parent organization of: Proteome Analyst is parent organization of: Proteome Analyst PA-GOSUB is parent organization of: CGView is parent organization of: UAlberta Cell Imaging Centre is parent organization of: UAlberta Institute for Biomolecular Design is parent organization of: UAlberta Mass Spectrometry Facility - Department of Chemistry is parent organization of: University of Alberta Labs and Facilities is parent organization of: CCDB - The CyberCell Database is parent organization of: VKCDB - Voltage-gated K Channel Database is parent organization of: Human Metabolome Database is parent organization of: Proteome Analyst is parent organization of: Neuromembrane Simulator is parent organization of: MetaboAnalyst is parent organization of: MetaboAnalyst is parent organization of: Alberta University Diabetes Institute IsletCore Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Transgenic Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Lipidomics Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Flow Cytometry Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Cell Imaging Centre Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Autoclave Repair Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry Workshop Core Facility is parent organization of: University of Alberta Faculty of Medicine and Dentistry High Content Analysis Core Facility is parent organization of: University of Alberta Precision Human Health Laboratory Core Facility provides: Heatmapper |
Free, Freely available | nlx_10148 | SCR_001853 | University of Alberta | 2026-02-07 02:05:45 | 7 | ||||||||
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SamSPECTRAL Resource Report Resource Website 1+ mentions |
SamSPECTRAL (RRID:SCR_001858) | software resource | Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample. | software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry, stem cell, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Cancer, HIV | PMID:20667133 | Free, Available for download, Freely available | OMICS_05638, biotools:samspectral | https://bio.tools/samspectral | SCR_001858 | SamSPECTRAL - Identifies cell population in flow cytometry data | 2026-02-07 02:05:37 | 4 |
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