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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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JaBba Resource Report Resource Website 1+ mentions |
JaBba (RRID:SCR_027134) | software application, software resource | Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments). | Builds genome graph, junctions and read depth, infer junction-balanced genome graphs, whole genome sequencing, inferring optimal copy numbers, vertices and edges, DNA segments, bonds between segments, | NCI P01 CA91955; NCI P30 CA015704 |
PMID:33007263 | Free, Available for download, Freely available, | SCR_027134 | Junction Balance Analysis | 2026-02-15 09:24:09 | 1 | ||||||||
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Palantir Resource Report Resource Website 1+ mentions |
Palantir (RRID:SCR_027194) | source code, algorithm resource, software resource | Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state. | Trajectory, align cells along differentiation trajectories, | NICHD DP1-HD084071; NCI R01CA164729; NCI P30 CA008748 |
PMID:30899105 | Free, Available for download, Freely available | SCR_027194 | 2026-02-15 09:23:31 | 3 | |||||||||
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SeSAMe Resource Report Resource Website 10+ mentions |
SeSAMe (RRID:SCR_027388) | SeSAMe | software toolkit, software resource | Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions. | reducing artifactual detection, DNA methylation, Infinium BeadChips, genomic deletions, | NCI U24 CA143882; NCI R01 CA170550; NCI U24 CA210969; Ovarian Cancer Research Fund Grant ; Michelle Lunn Hope Foundation ; Van Andel Research Institute |
PMID:30085201 | Free, Available for download, Freely available, | SCR_027388 | SEnsible Step-wise Analysis of DNA MEthylation | 2026-02-15 09:24:18 | 18 | |||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, source code, software resource | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIMH R01 MH101244; NIGMS R01 GM078598 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE http://genetics.bwh.harvard.edu/cbase |
SCR_027765 | Cancer Bayesian SElection estimation | 2026-02-15 09:23:36 | 0 | |||||||
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T Cell ExTRECT Resource Report Resource Website |
T Cell ExTRECT (RRID:SCR_027742) | source code, software toolkit, software resource | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NHLBI U54HL108460; NCATS UL1TR000100; NCI R21CA177519; NCI P30CA023100; NCI U01CA196406; NLM T15LM011271; NIH Office of the Director DP5OD017937; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-02-15 09:24:11 | 0 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, source code, software toolkit, software resource | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NSF ; NIGMS T32 GM008313; NCI R37 CA222574; NCI R01 CA227388; NCI U01 CA233100 |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-02-15 09:24:20 | 2 | |||||||||
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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software application, software resource | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-02-15 09:24:13 | 0 | ||||||||
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OligoGenome Resource Report Resource Website 1+ mentions |
OligoGenome (RRID:SCR_006025) | OligoGenome | data or information resource, database, resource | The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets. | oligonucleotide, genome, probe, coding region, oligonucleotide sequence, chromosome | has parent organization: Stanford University; Stanford; California | NHGRI RC2 HG005570-01; NCI R21CA12848; NCI 5K08CA96879?6; NIDDK DK56339; NHGRI 2P01HG000205; NLM T15-LM007033; Doris Duke Clinical Foundation ; Reddere Foundation ; Liu Bie Ju Cha and Family Fellowship in Cancer ; Wang Family Foundation ; Howard Hughes Medical Foundation |
PMID:22102592 | nlx_151422 | SCR_006025 | Stanford Human Oligo Genome Project, Human OligoGenome Resource, Stanford Human Oligo Genome, Human Oligo Genome, Human OligoGenome | 2026-02-14 02:01:13 | 2 | ||||||
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DupRecover Resource Report Resource Website |
DupRecover (RRID:SCR_006410) | DupRecover | software resource | Software that facilitates accurate estimation for sampling-induced read duplication in deep sequencing experiments. | python, overcorrection, variant, allele fraction, copy number variation |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center has parent organization: Bitbucket |
MD Anderson Odyssey recruitment fellowship ; The MD Anderson Cancer Center Sheikh Khalifa Ben Zayed Al Nahyan Institute of Personalized Cancer Therapy ; NCI R01CA172652-01; NCI P30CA016672 |
PMID:24389657 | Free, Public | OMICS_02201 | SCR_006410 | 2026-02-14 02:01:07 | 0 | ||||||
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PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 500+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | knowledge environment resource, data or information resource, portal | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-02-14 02:00:09 | 903 | ||||
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Drug Target Ontology Resource Report Resource Website 1+ mentions |
Drug Target Ontology (RRID:SCR_015581) | DTO | data or information resource, ontology, controlled vocabulary | Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. | drug ontology, drug target ontology, protein family | has parent organization: University of Miami; Florida; USA | NCI U54CA189205; NHLBI U54HL127624 |
Available for download | https://github.com/DrugTargetOntology/DTO http://bioportal.bioontology.org/ontologies/DTO | SCR_015581 | Drug Target Ontology (DTO) | 2026-02-14 02:03:03 | 2 | ||||||
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nanoPOTS Resource Report Resource Website 1+ mentions |
nanoPOTS (RRID:SCR_017129) | instrument resource | Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes. | nanodroplet, processing, platform, quantitative, proteome, profiling, analysis, mammalian, cell, small, volume | has parent organization: Pacific Northwest National Laboratory | NIBIB R21 EB020976; NCI R33 CA225248; NIGMS P41 GM103493; NIDDK UC4 DK104167; NIDDK DP3 DK110844; NIH Office Of The Director S10 OD016350; JDRF |
PMID:29491378 | SCR_017129 | 2026-02-14 02:03:08 | 1 | |||||||||
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Add Health (National Longitudinal Study of Adolescent Health) Resource Report Resource Website 10+ mentions |
Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) | Add Health | data or information resource, database | Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database. | adolescent, longitudinal, adult human, interview, social, behavior, health, early adult human, FASEB list | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Aging | NICHD ; NCI ; CDC ; NIAID ; NIMHD ; NIDCD ; NIGMS ; NIMH ; NINR ; NIA ; NIAAA ; NIDA ; NSF ; NIH ; Department of Health and Human Services ; MacArthur Foundation ; Robert Wood Johnson Foundation |
Restricted use | nif-0000-00621 | SCR_007434 | National Longitudinal Study of Adolescent Health | 2026-02-14 02:06:03 | 37 | |||||
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Open Regulatory Annotation Database Resource Report Resource Website 50+ mentions |
Open Regulatory Annotation Database (RRID:SCR_007835) | ORegAnno | data or information resource, database | Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation. | Collection, annotation, curated, experimentally, identified, DNA, regulatory, region, element, transcript, factor, binding, site, regulatory, variant, data, FASEB list |
has parent organization: University of Manchester; Manchester; United Kingdom works with: PubMed works with: Entrez Gene works with: Ensembl works with: dbSNP |
British Columbia Cancer Foundation ; Genome Canada ; Genome British Columbia ; European Network of Excellence ; BioSapiens Network of Excellence ; Research Foundation – Flanders ; Pleiades Promoter Project ; Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research ; European Molecular Biology Laboratory ; Marie Curie Early Stage Research Training Fellowship ; Natural Sciences and Engineering Research Council ; Swedish Research Council ; American Cancer Society ; Edward Mallinckrodt ; Jr. Foundation ; NHGRI K99 HG007940; NHGRI R01 HG008150; NIMH R01 MH101814; NCI K22 CA188163 |
PMID:18006570 PMID:26578589 |
Free, Freely available | nif-0000-03223, r3d100010656 | http://www.oreganno.org/ https://doi.org/10.17616/R3DG70 |
SCR_007835 | Open REGulatory ANNOtation, ORegAnno 3.0 | 2026-02-14 02:06:39 | 81 | ||||
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caHUB Resource Report Resource Website |
caHUB (RRID:SCR_009657) | caHUB | data or information resource, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures. | biospecimen, clinical, biomaterial supply resource, tissue |
is listed by: NIDDK Information Network (dkNET) is related to: Biorepositories and Biospecimens Research Branch has parent organization: National Cancer Institute |
Cancer | NCI ; ARRA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156094 | SCR_009657 | The Cancer Human Biobank, cancer Human Biobank | 2026-02-14 02:05:05 | 0 | |||||
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SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-02-14 02:06:25 | 740 | |||||
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Transcriptional Regulatory Element Database Resource Report Resource Website 50+ mentions |
Transcriptional Regulatory Element Database (RRID:SCR_005661) | TRED | data or information resource, database | Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated. | Mammalian, cis, trans, regulatory, element, mapped, genome, gene, regulation, function, data, FASEB list |
uses: GenBank uses: Eukaryotic Promoter Database uses: DBTSS: Database of Transcriptional Start Sites has parent organization: Cold Spring Harbor Laboratory |
NCI ; NHGRI HG001696 |
PMID:17202159 | Free, Freely available | nif-0000-03585 | SCR_005661 | Transcriptional Regulatory Element Database | 2026-02-14 02:05:57 | 78 | |||||
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Mouse Tumor Biology Database Resource Report Resource Website 1+ mentions |
Mouse Tumor Biology Database (RRID:SCR_006517) | MTB | data or information resource, database | Database supports use of mouse model system for human cancer by providing comprehensive resource for data and information on various tumor models. | endogenous, knock out mouse, hybrid, inbred mouse strain, induced, mouse, mutant, pathology, tumor, gene, organ, strain, genetics, pathology, image, gene expression |
is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
Cancer, Tumor, Hereditary cancer | NCI CA089713 | PMID:18432250 PMID:21282667 |
The community can contribute to this resource, Acknowledgement requested, For research and educational purposes, Non-commercial, Without the prior express written permission | nif-0000-03163, SCR_017516 | http://tumor.informatics.jax.org/mtbwi/index.do | SCR_006517 | MGI: MTB Database, Mouse Tumor Biology (MTB) Database, MTB Database, MTB: Mouse Tumor Biology Database | 2026-02-14 02:06:26 | 8 | |||
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Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes Resource Report Resource Website 1+ mentions |
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) | data or information resource, data set | Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. | molecular, taxonomy, lung, carcinoma, cancer, death, mrna, expression, sequence, data, adenocarcinoma, neuroendocrine, gene, type ii pneumocyte, analysis, metastasis, integration, mrna expression profiling | has parent organization: Broad Institute | Lung cancer | NCI U01 CA84995 | PMID:11707567 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30292 | SCR_003010 | Cancer Genomics Publication | 2026-02-14 02:07:20 | 2 | |||||
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National Longitudinal Mortality Study Resource Report Resource Website 10+ mentions |
National Longitudinal Mortality Study (RRID:SCR_008946) | NLMS | data or information resource, data set | A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134 | national, longitudinal, mortality, demographic, socio-economic, age, cause of death, death, death record, ethnicity, mortality rate, gender, marital status, race, late adult human, FASEB list |
is listed by: Inter-university Consortium for Political and Social Research (ICPSR) has parent organization: U.S. Census Bureau |
Aging | NCI ; NHLBI ; NIA ; National Center for Health Statistics ; U.S. Census Bureau |
Public | nlx_151861 | SCR_008946 | National Longitudinal Mortality Study (NLMS) | 2026-02-14 02:07:24 | 32 |
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