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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Spark Resource Report Resource Website 100+ mentions |
Spark (RRID:SCR_006207) | Spark | data analysis software, data processing software, data visualization software, software application, software resource | A clustering and visualization tool that enables the interactive exploration of genome-wide data, with a specialization in epigenomics data. Spark is also available as a service within the Epigenome toolset of the Genboree Workbench. The approach utilizes data clusters as a high-level visual guide and supports interactive inspection of individual regions within each cluster. The cluster view links to gene ontology analysis tools and the detailed region view connects to existing genome browser displays taking advantage of their wealth of annotation and functionality. | epigenomics, genome browser, clustering, visualization, genome, computation, pattern discovery, cluster |
is related to: Genboree Discovery System is related to: Roadmap Epigenomics Project has parent organization: BC Cancer Agency |
Canadian Institutes of Health Research ; Michael Smith Foundation for Health Research ; Natural Sciences and Engineering Research Council of Canada ; NIDA U01 DA025956; NIEHS 5U01ES017154-02; NHGRI HG004558 |
PMID:22960372 | Available for download without charge. Please cite. | nlx_151753 | SCR_006207 | Sparkinsight | 2026-08-21 12:37:44 | 417 | |||||
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Roadmap Epigenomics Project Resource Report Resource Website 100+ mentions |
Roadmap Epigenomics Project (RRID:SCR_008924) | Roadmap Epigenomics Project | consortium, data or information resource, organization portal, portal, project portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11, 2022. Project for human epigenomic data from experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent normal counterparts of tissues and organ systems frequently involved in human disease. Consortium expects to deliver collection of normal epigenomes that will provide framework or reference for comparison and integration within broad array of future studies. Consortium is also committed to development, standardization and dissemination of protocols, reagents and analytical tools to enable research community to utilize, integrate and expand upon this body of data. | epigenomics, genome, genetic variation, gene regulation, genomics, stem cell, primary cell, tissue, blood, lung, heart, gastrointestinal tract, brain, embryonic stem cell, fetus, adult, cell, epigenome, methylome, chip-seq, rna, breast, muscle, connective, gastrointestinal, genitourinary, fat, hematopoietic stem cell, thymus, spleen, placenta, kidney, adrenal, induced pluripotent stem cell, skin, angular gyrus, anterior caudate, cingulate gyrus, hippocampus, inferior temporal lobe, mid frontal lobe, substantia nigra, dna methylation, histone modification, chromatin, rna transcript, dna, methylation, histone, data set |
is used by: NIF Data Federation is used by: VizHub is used by: Integrated Data Annotation is listed by: 3DVC is listed by: OMICtools is related to: NCBI Epigenomics is related to: Gene Expression Omnibus is related to: Spark is related to: Deep Blue Epigenomic Data Server has parent organization: NIH Common Fund is parent organization of: Human Epigenome Atlas is parent organization of: WashU Epigenome Browser is parent organization of: VizHub |
PMID:22690667 PMID:20944595 PMID:20944597 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151644, OMICS_01564 | SCR_008924 | Epigenomics Program, Common Fund Epigenomics, NIH Roadmap Epigenomics Program, NIH Roadmap Epigenomics Project, Common Fund Epigenomics Program, NIH Common Fund Epigenomics, NIH Common Fund Epigenomics Program, Common Fund Roadmap Epigenomics Program | 2026-08-21 12:38:48 | 323 | ||||||
|
Genboree Discovery System Resource Report Resource Website 10+ mentions |
Genboree Discovery System (RRID:SCR_000747) | Genboree | data or information resource, data processing software, database, software application, software resource | A software application and database viewing system for genomic research, more specifically formulti-genome comparison and pattern discovery via genome self-comparison. Data are available for a range of species including Human Chr3, Human Chr12, Sea Urchin, Tribolium, and cow. The Genboree Discovery System is the largest software system developed at the bioinformatics laboratory at Baylor in close collaboration with the Human Genome Sequencing Center. Genboree is a turnkey software system for genomic research. Genboree is hosted on the Internet and, as of early 2007, the number of registered users exceeds 600. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison. Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps. Our Positional Hashing method, implemented in the Pash program, enables extremely fast and accurate sequence comparison and pattern discovery by employing low-level parallelism. Pash enables fast and sensitive detection of orthologous regions across mammalian genomes, and fast anchoring of hundreds of millions of short sequences produced by next-generation sequencing technologies. We are further developing the Pash program and employing it in the context of various discovery pipelines. Our laboratory participates in the pilot stage of the TCGA (The Cancer Genome Atlas) project. We aim to develop comprehensive, rapid, and economical methods for detecting recurrent chromosomal aberrations in cancer using next-generation sequencing technologies. The methods will allow detection of recurrent chromosomal aberrations in hundreds of small ( | genome, genomic, next generation sequencing |
is related to: Spark has parent organization: Baylor University; Texas; USA |
nif-0000-08906 | SCR_000747 | Genboree Discovery System | 2026-08-21 12:36:15 | 11 | ||||||||
|
BC Cancer Agency Resource Report Resource Website 1+ mentions |
BC Cancer Agency (RRID:SCR_004201) | BCCA | institution | A portal that provides a province-wide, population-based cancer control program for the residents of British Columbia and the Yukon. The BC Cancer Agency''s mandate covers the spectrum of cancer care, from prevention and screening, to diagnosis, treatment, and through to rehabilitation. The BC Cancer Agency''s mandate is driven by a three-fold mission: 1. To reduce the incidence of cancer; 2. To reduce the mortality rate of people with cancer; 3. To improve the quality of life of people living with cancer. This mission drives everything we do, including providing screening, diagnosis and care, setting treatment standards, and conducting research into causes of, and cures for, cancer. The BC Cancer Agency operates five regional cancer centers, providing assessment and diagnostic services, chemotherapy, radiation therapy, and supportive care. Each of the BC Cancer Agency''s centers delivers cancer treatment based on provincial standards and guidelines established by the Agency. We work in partnership with communities to provide a network of chemotherapy clinics so patients can receive care closer to home. Research is an essential part of the BC Cancer Agency''s mission to not only find the causes of cancer, but to find better treatments for prolonged life and better quality of life. With direct links between the BC Cancer Agency''s physicians and researchers at our five centers, the Deeley Research Centre (located in Victoria) and the BC Cancer Agency''s Research Centre (located in Vancouver), we can quickly translate new discoveries into clinical applications. The BC Cancer Agency''s Research Centre includes eight specialty laboratories including the Genome Sciences Centre, and the Terry Fox Laboratory. The BC Cancer Foundation raises funds for cancer research and enhancements to care at the BC Cancer Agency. |
is related to: BC Cancer Foundation is parent organization of: cisRED: cis-regulatory element is parent organization of: British Columbia Gynaecologic Tissue Bank is parent organization of: British Columbia Tumour Tissue Repository is parent organization of: Spark is parent organization of: ALEA is parent organization of: APOLLOH is parent organization of: British Columbia Breast Cancer Tumour Bank is parent organization of: JointSNVMix is parent organization of: mutationSeq is parent organization of: Mouse Gene Expression at the BC Cancer Agency is parent organization of: C. elegans Resources is parent organization of: BCCA Cancer Drug Manual is parent organization of: flowCL is parent organization of: flowBin |
Cancer | BC Cancer Foundation | ISNI: 0000 0001 0702 3000, Wikidata: Q4835275, grid.248762.d, nlx_143635, Crossref funder ID: 501100005614 | https://ror.org/03sfybe47 | SCR_004201 | British Columbia Cancer Agency | 2026-08-21 12:37:23 | 3 |
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