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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Newcastle University; Newcastle upon Tyne; United Kingdom Resource Report Resource Website 1+ mentions |
Newcastle University; Newcastle upon Tyne; United Kingdom (RRID:SCR_012923) | Newcastle University | university | UK public research university based in Newcastle upon Tyne, North East England with overseas campuses in Singapore and Malaysia. The university is a red brick university and a member of the Russell Group, an association of research-intensive UK universities. |
is parent organization of: Code Analysis Repository and Modelling for e-Neuroscience is parent organization of: eDoctoring is parent organization of: SINOMO is parent organization of: DONE: Detection of Outlier NEurons is parent organization of: HUDSEN is parent organization of: Human Developmental Biology Resource is parent organization of: Newcastle University Bioinformatics Support Unit is parent organization of: Newcastle University Labs and Facilities is parent organization of: HUDSEN Electronic Atlas of the Developing Human Brain is parent organization of: JEPETTO is parent organization of: Newcastle Brain Tissue Resource is parent organization of: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) is parent organization of: Newcastle University Bioimaging Unit Core Facility |
grid.1006.7, nlx_51333, Crossref funder ID:501100008406, Wikidata:Q837164, ISNI:0000 0001 0462 7212 | https://ror.org/01kj2bm70 | SCR_012923 | Newcastle University; Newcastle; United Kingdom, Newcastle University; Newcastle-upon-Tyne; United Kingdom | 2026-08-01 12:04:42 | 4 | ||||||||
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NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases Resource Report Resource Website 100+ mentions |
NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases (RRID:SCR_012895) | NIDDK | government granting agency | Center with mission to conduct and support medical research and research training and to disseminate science-based information on diabetes and other endocrine and metabolic diseases. The NIDDK supports a wide range of medical research through grants to universities and other medical research institutions across the country. | diabetes, metabolic disease, digestive, kidney, endocrine, medical research |
recommends: Cell Image Library (CIL) recommends: Biological General Repository for Interaction Datasets (BioGRID) recommends: NIDDK Central Repository recommends: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) recommends: Metabolomics Workbench recommends: PeptideAtlas recommends: Network Data Exchange (NDEx) recommends: Mouse Genome Informatics (MGI) recommends: Zebrafish Information Network (ZFIN) recommends: FlyBase recommends: Database of Interacting Proteins (DIP) recommends: WormBase recommends: PhysioNet recommends: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) recommends: UniProt recommends: dbSNP recommends: DNA DataBank of Japan (DDBJ) recommends: European Nucleotide Archive (ENA) recommends: dbVar recommends: ClinicalTrials.gov recommends: European Variation Archive (EVA) recommends: MGnify recommends: Analysis, Visualization, and Informatics Lab-space (AnVIL) recommends: GenBank recommends: Gene Expression Omnibus (GEO) recommends: miRBase recommends: Database of Genomic Variants Archive (DGVa) recommends: Crystallography Open Database (COD) recommends: Coherent X-Ray Imaging Data Bank (CXIDB) recommends: Biological Magnetic Resonance Data Bank (BMRB) recommends: Worldwide Protein Data Bank (wwPDB) recommends: EMDataResource.org recommends: NCBI Assembly Archive Viewer recommends: Cambridge Crystallographic Data Centre (CCDC) recommends: Inorganic Crystal Structure Database (ICSD) recommends: Structural Biology Grid recommends: ArrayExpress recommends: GenomeRNAi recommends: NCBI database of Genotypes and Phenotypes (dbGap) recommends: Protein Circular Dichroism Data Bank (PCDDB) recommends: Electron Microscopy Data Bank at PDBe (MSD-EBI) recommends: PDBe - Protein Data Bank in Europe recommends: PubChem BioAssay recommends: Japanese Genotype-phenotype Archive (JGA) recommends: ProteomeXchange recommends: IntAct recommends: European Genome phenome Archive recommends: MetaboLights recommends: PubChem Substance recommends: The Immunology Database and Analysis Portal (ImmPort) recommends: STRENDA recommends: Kinetic Models of Biological Systems (KiMoSys) recommends: FLOWRepository recommends: Mass spectrometry Interactive Virtual Environment (MassIVE) recommends: Global Proteome Machine Database (GPM DB) recommends: Cancer Imaging Archive (TCIA) recommends: German Neuroinformatics Node (G-Node) recommends: 1000 Functional Connectomes Project recommends: ChEMBL recommends: Image Data Resource (IDR) recommends: SICAS Medical Image Repository recommends: ZENODO recommends: Dataverse Network Project recommends: NeuroMorpho.Org recommends: Mendeley Data recommends: NIMH Data Archive recommends: NIH Figshare Archive recommends: FigShare recommends: National Addiction and HIV Data Archive Program (NAHDAP) recommends: Dryad Digital Repository recommends: Open Science Framework recommends: OpenNeuro recommends: SPARC Portal lists: Mutant Mouse Resource and Research Center lists: NIDDK Research Resources is affiliated with: Cystic Fibrosis Research and Translation Centers is affiliated with: Nutrition and Obesity Research Centers is affiliated with: O'Brien Urology Centers is affiliated with: Hematology Centers is affiliated with: Polycystic Kidney Disease Research and Translation Centers is affiliated with: O'Brien Kidney Centers is affiliated with: Diabetes Research Centers is affiliated with: Digestive Disease Centers is affiliated with: Centers for Diabetes Translation Research is affiliated with: Pediatric Centers of Excellence in Nephrology is affiliated with: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study is related to: Bridging Interventional Development Gaps is related to: Polycystic Kidney Disease Research Resource Consortium has parent organization: National Institutes of Health is parent organization of: MTOPS Prostate Samples Analysis Consortium is parent organization of: Symptom Score for Benign Prostatic Hyperplasia is parent organization of: Type 1 Diabetes - Rapid Access to Intervention Development is parent organization of: National Diabetes Education Program is parent organization of: Family Investigation of Nephropathy of Diabetes is parent organization of: Frequent Hemodialysis Network Daily Trial is parent organization of: HemBase is parent organization of: NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources is parent organization of: dkCOIN is parent organization of: National Kidney Disease Education Program is parent organization of: Network of Minority Health Research Investigators is parent organization of: National Endocrine and Metabolic Diseases Information Service is parent organization of: National Diabetes Information Clearinghouse is parent organization of: National Digestive Diseases Information Clearinghouse is parent organization of: National Hematologic Diseases Information Service is parent organization of: National Kidney and Urologic Diseases Information Clearinghouse is parent organization of: Type 1 Diabetes Preclinical Testing Program is parent organization of: Frequent Hemodialysis Network Nocturnal Trial is parent organization of: Boston Area Community Health Survey is parent organization of: Minimally Invasive Surgical Therapies Treatment Consortium for Benign Prostatic Hyperplasia is parent organization of: Focal Segmental Glomerulosclerosis in Children and Young Adults Interventional Study |
Type 1 diabetes, Type 2 diabetes, Diabetes, Digestive disease, Kidney disease, Endocrine disease, Obesity, Blood disease, Liver disease, Urologic disease | nlx_inv_1005102 | SCR_012895 | National Institute of Diabetes and Digestive and Kidney Diseases | 2026-08-01 12:04:41 | 140 | |||||||
|
BRAINSTracer Resource Report Resource Website 1+ mentions |
BRAINSTracer (RRID:SCR_012894) | BRAINSTracer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A graphical program to trace anatomical features in 3D image volumes. This tools is built upon the NA-MIC toolkit. The tool is fully compatible with Slicer3, and integrates the Slicer3 theme. | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: BRAINSTools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155705 | http://www.nitrc.org/projects/brainstracer | SCR_012894 | 2026-08-01 12:04:42 | 5 | |||||||
|
National Science Foundation Resource Report Resource Website 1000+ mentions |
National Science Foundation (RRID:SCR_012938) | NSF | institution | An independent federal agency created by Congress to promote the progress of science; to advance the national health, prosperity, and welfare; to secure the national defense They are the funding source for approximately 20 percent of all federally supported basic research conducted by America''s colleges and universities. In many fields such as mathematics, computer science and the social sciences, NSF is the major source of federal backing. NSF leadership has two major components: a director who oversees NSF staff and management responsible for program creation and administration, merit review, planning, budget and day-to-day operations; and a 24-member National Science Board (NSB) of eminent individuals that meets six times a year to establish the overall policies of the foundation.The director and all Board members serve six year terms. Each of them, as well as the NSF deputy director, is appointed by the President of the United States and confirmed by the U.S. Senate. At present, NSF has a total workforce of about 2,100 at its Arlington, Va., headquarters, including approximately 1,400 career employees, 200 scientists from research institutions on temporary duty, 450 contract workers and the staff of the NSB office and the Office of the Inspector General. NSF is the only federal agency whose mission includes support for all fields of fundamental science and engineering, except for medical sciences. They are tasked with keeping the United States at the leading edge of discovery in areas from astronomy to geology to zoology. So, in addition to funding research in the traditional academic areas, the agency also supports high-risk, high pay-off ideas, novel collaborations and numerous projects that may seem like science fiction today, but which the public will take for granted tomorrow. And in every case, they ensure that research is fully integrated with education so that today''s revolutionary work will also be training tomorrow''s top scientists and engineers NSF''s task of identifying and funding work at the frontiers of science and engineering is not a top-down process. |
is related to: DMPTool is parent organization of: NSDL: The National Science Digital Library is parent organization of: CIPRES Science Gateway is parent organization of: dCAPS Finder is parent organization of: Scholarpedia is parent organization of: Chlamydomonas Resource Center is parent organization of: Bacillus Genetic Stock Center (BGSC) is parent organization of: Sheep Brain Atlas is parent organization of: Advanced Cyberinfrastructure Coordination Ecosystem Services and Support Core Facility |
grid.431093.c, Wikidata: Q304878, ISNI: 0000 0001 1958 7073, Crossref funder ID: 100000001, nlx_inv_1005118 | https://ror.org/021nxhr62 | SCR_012938 | National Science Foundation | 2026-08-01 12:04:43 | 2070 | ||||||||
|
DNaseR Resource Report Resource Website |
DNaseR (RRID:SCR_012819) | DNaseR | software resource | A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:23118738 | Free | biotools:dnaser, OMICS_00517 | https://bio.tools/dnaser | SCR_012819 | DNaseR: DNase I footprinting analysis of DNase-seq data | 2026-08-01 12:04:40 | 0 | |||||
|
Acacia Resource Report Resource Website 100+ mentions |
Acacia (RRID:SCR_012896) | Acacia | software resource | Accurate error-correction of amplicon pyrosequences. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
DOI:10.1038/nmeth.1990 | OMICS_01116 | https://sources.debian.org/src/acacia/ | SCR_012896 | 2026-08-01 12:04:53 | 106 | ||||||||
|
Abcam Resource Report Resource Website 10000+ mentions |
Abcam (RRID:SCR_012931) | commercial organization, antibody supplier, reagent supplier, material resource | A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits. | antibody supplier, rabmabs, epitomics, immunoassay, primary antibody, secondary antibody |
is affiliated with: MitoScience is parent organization of: Epitomics |
Available to the research community | nlx_152244 | SCR_012931 | 2026-08-01 12:04:41 | 115565 | |||||||||
|
TargetScore Resource Report Resource Website 1+ mentions |
TargetScore (RRID:SCR_012933) | TargetScore | software resource | Software to infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24135265 | Free | OMICS_00421 | SCR_012933 | TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information | 2026-08-01 12:04:53 | 3 | |||||||
|
OncoSNP Resource Report Resource Website 10+ mentions |
OncoSNP (RRID:SCR_012985) | OncoSNP | software resource | An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data. | is listed by: OMICtools | Cancer | Freely available for academic use, Non-commercial, Commercial with permission | OMICS_00728 | SCR_012985 | 2026-08-01 12:04:54 | 19 | ||||||||
|
RLMM Resource Report Resource Website 1+ mentions |
RLMM (RRID:SCR_012984) | RLMM | software resource | A Genotype Calling Algorithm for Affymetrix SNP Arrays. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00732 | SCR_012984 | 2026-08-01 12:04:44 | 5 | ||||||||||
|
Zebra Finch Expression Brain Atlas Resource Report Resource Website 10+ mentions |
Zebra Finch Expression Brain Atlas (RRID:SCR_012988) | ZEBrA | expression atlas, atlas, data or information resource, database | Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches. | gene, expression, brain, in-situ, hybridization, taeniopygia, vocal learning, anatomical, atlas, data set, molecular neuroanatomy, adult, male, gene, image, bird, image, avian | has parent organization: Oregon Health and Science University; Oregon; USA | NINDS R03 NS059755; NIGMS R24 GM092842 |
Free, Freely available | nif-0000-24345, SCR_000641, nlx_152091 | http://ignrhnet.ohsu.edu/finch/songbird/index.php | SCR_012988 | zebra, , Zebra Finch Expression Brain Atlas, atlas, Zebra Finch Brain Atlas, ZEBrA, finch | 2026-08-01 12:04:54 | 38 | |||||
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IBDLD Resource Report Resource Website 10+ mentions |
IBDLD (RRID:SCR_013043) | IBDLD | software resource | A C++ software program for multipoint IBD estimation based on high density SNP genotype data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21769932 | Free | OMICS_00204 | SCR_013043 | 2026-08-01 12:04:55 | 14 | |||||||
|
SolSNP Resource Report Resource Website 1+ mentions |
SolSNP (RRID:SCR_013045) | SolSNP | software resource | A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. |
is listed by: OMICtools has parent organization: SourceForge |
MIT License | OMICS_00079 | SCR_013045 | 2026-08-01 12:04:55 | 7 | |||||||||
|
HATS Resource Report Resource Website 10+ mentions |
HATS (RRID:SCR_013044) | HATS | software resource | A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00200 | SCR_013044 | Haplotype Amplification in Tumor Sequences | 2026-08-01 12:04:45 | 37 | |||||||||
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charm Resource Report Resource Website 50+ mentions |
charm (RRID:SCR_012992) | charm | software resource | Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:charm, OMICS_00792 | https://bio.tools/charm | SCR_012992 | 2026-08-01 12:04:43 | 63 | ||||||||
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ChIPOTle Peak Finder Resource Report Resource Website |
ChIPOTle Peak Finder (RRID:SCR_012991) | ChIPOTle Peak Finder | software resource | A peak-finding algorithm used to analyze ChIP-chip microarray data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00803 | SCR_012991 | 2026-08-01 12:04:54 | 0 | ||||||||||
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Multivariate Analysis of Transcript Splicing Resource Report Resource Website 100+ mentions |
Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) | MATS | data processing software, data analysis software, software application, software resource | Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design. | Differential alternative splicing events, splicing events calculation, RNA-Seq data, gene isoform ratio, alternative splicing patterns, patterns detection, patterns analysis, replicate RNA-Seq data |
is listed by: OMICtools is listed by: SourceForge has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA |
Free, Available for download, Freely available | OMICS_01336, SCR_020941 | SCR_013049 | RNAseq MATS, RMATS, rMATS, MATS, RNA MATS | 2026-08-01 12:04:45 | 192 | |||||||
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BiSeq Resource Report Resource Website 10+ mentions |
BiSeq (RRID:SCR_012993) | BiSeq | software resource | Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00620 | SCR_012993 | 2026-08-01 12:04:44 | 30 | ||||||||||
|
Trinity Resource Report Resource Website 5000+ mentions |
Trinity (RRID:SCR_013048) | Trinity | software resource | Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Broad Institute has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1038/nbt.1883 | biotools:trinity, OMICS_01327 | https://bio.tools/trinity, https://sources.debian.org/src/trinityrnaseq/ | SCR_013048 | 2026-08-01 12:04:55 | 9576 | |||||||
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NGSpeAnalysis Resource Report Resource Website |
NGSpeAnalysis (RRID:SCR_013040) | NGSpeAnalysis | software resource | A pipeline using open-source tools which can implement a set of pair ended Next-generation sequencing analysis, include short reads alignment, high-quality variation genotype calling and variants annotation. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00291 | SCR_013040 | 2026-08-01 12:04:44 | 0 |
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