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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DREME Resource Report Resource Website 10+ mentions |
DREME (RRID:SCR_016860) | analysis service resource, data analysis service, production service resource, service resource | Software tool to discover short, ungapped motifs (recurring, fixed-length patterns) that are relatively enriched in sequences compared with shuffled sequences or control sequences (sample output from sequences). | discover, short, ungapped, motif, sequence, compare, shuffled, control, sample, output, recurring, fixed, length, pattern, data | is listed by: MEME Suite - Motif-based sequence analysis tools | Free, Available for download, Freely avaialble | SCR_016860 | Discriminative Regular Expression Motif Elicitation, DREME | 2026-09-19 12:57:36 | 23 | |||||||||
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COLLECT database Resource Report Resource Website 1+ mentions |
COLLECT database (RRID:SCR_018366) | data or information resource, database | Collaborative database for pregnancy and placental research studies worldwide by Global Pregnancy Collaboration CoLab . Database for collecting data for pregnancy studies in preeclampsia and other fields. Database has web based data entry platform with study specific user access. Data can also be entered offline using formatted spreadsheet template that can be uploaded to database in bulk or stored locally. Data is property of investigator but with permission can be combined into larger studies across centers and countries. Collaboration is enabled but not required. | Placenta, preeclampsia, obstetrics, perinatal research, data, data set, pregnancy, Global Pregnancy Collaboration, CoLab | preeclampsia | Bill and Melinda Gates Foundation | PMID:29978556 PMID:28864015 |
Restricted | SCR_018366 | 2026-09-19 12:57:37 | 1 | ||||||||
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Molecular Signatures Database Resource Report Resource Website 1000+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NCI CA295532; NIGMS ; NIH |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-09-19 12:57:36 | 1702 | ||||||
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VA Phenomics Library Resource Report Resource Website 1+ mentions |
VA Phenomics Library (RRID:SCR_019107) | VAPheLib | data or information resource, database | Shared knowledgebase of VA EHR-based phenotype algorithms, definitions and data curation metadata. | Phenomics library, centralized phenomics VA library, data, curation metadata, phenotype | https://www.hsrd.research.va.gov/for_researchers/cyber_seminars/archives/3814-notes.pdf | SCR_019107 | 2026-09-19 12:57:38 | 1 | ||||||||||
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Research Information Network Resource Report Resource Website |
Research Information Network (RRID:SCR_000931) | data or information resource, narrative resource | A network resource that aims to enhance and broaden understanding of how researchers in the UK create and use information resources. The network provides services of all kinds to support the development of effective policies and practices for researchers, institutions, funders, information professionals and everyone who is involved in the information landscape. | information, data, network | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_77489 | http://www.rin.ac.uk/blogs/team | SCR_000931 | Research Information Network | 2026-09-19 12:57:43 | 0 | ||||||||
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Cerebellar Platform Resource Report Resource Website 1+ mentions |
Cerebellar Platform (RRID:SCR_001700) | Cerebellar Platform | software repository, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation. | electrophysiology, function, analysis, cerebellar, data, imaging, mathematical, model, molecular biology, paper, plasticity, program, review, script, structure, theory, book, cerebellum |
is used by: NIF Data Federation is related to: Integrated Software has parent organization: RIKEN Brain Science Institute |
Japan Society for the Promotion of Science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10193 | SCR_001700 | 2026-09-19 12:57:44 | 1 | |||||||
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Telethon Network of Genetic Biobanks Resource Report Resource Website 10+ mentions |
Telethon Network of Genetic Biobanks (RRID:SCR_004658) | TNGB | biomaterial supply resource, material resource | Network of non profit association of Italian repositories to form catalogue of biospecimens and associated data. Used to collect, process, preserve and distribute biological samples and related clinical data from individuals affected by rare diseases, their relatives or from healthy control individuals, with standards complying with Italian laws and international recommendations. You may browse sample catalogue by diagnosis or use advanced search option. Request for samples is granted only if project is in agreement with TNGB mission and after receiving signed material transfer agreement form. | Italian, repository, catalogue, biospeciment, data, collect, process, preserve, distribute, rare, disease |
is listed by: One Mind Biospecimen Bank Listing is affiliated with: EuroBioBank has parent organization: Telethon Foundation |
Italian Health Department ; Telethon Foundation |
PMID:24004821 | Restricted | nlx_65989 | SCR_004658 | Telethon Network of Genetic Biobanks | 2026-09-19 12:57:50 | 29 | |||||
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GenAge Resource Report Resource Website 100+ mentions |
GenAge (RRID:SCR_010223) | GenAge | data or information resource, database | Collection of annotated and manually curated data of genes related to aging divided into genes related to longevity and/or aging in model organisms (yeast, worms, flies, mice, etc.) and aging related human genes. | collection, curated, data, gene, aging, longevity |
is used by: GEROprotectors has parent organization: Human Ageing Genomic Resources |
Aging | HAGR''s lisense | nlx_156768 | SCR_010223 | GenAge, GenAge Database of Ageing-Related Genes, The Ageing Gene Database, Gene Database | 2026-09-19 12:57:21 | 157 | ||||||
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Alzforum Antibody Directory for Neuroscience Research Resource Report Resource Website |
Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) | data or information resource, database | The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations. | alzheimer, antibody, clinical trail, community, data, disease, disorder, molecule, neurodegenerative, protein, reagent, research, science, scientific, technology | has parent organization: Alzheimer's Research Forum | nif-0000-00129 | SCR_013601 | Alzforum Antibody Directory | 2026-09-19 12:57:31 | 0 | |||||||||
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Brain RNA-Seq Resource Report Resource Website 100+ mentions |
Brain RNA-Seq (RRID:SCR_013736) | data or information resource, database | Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. | RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain, FASEB list | has parent organization: Stanford University; Stanford; California | NIGMS T32GM007365; NIMH R01MH09955501; NINDS R01NS08170301 |
PMID:25186741 PMID:26687838 |
Free, Freely available | SCR_017483 | http://www.brainrnaseq.org/ | SCR_013736 | Barres Brain RNA-Seq | 2026-09-19 12:57:32 | 156 | |||||
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Cocoframer Resource Report Resource Website 1+ mentions |
Cocoframer (RRID:SCR_023817) | software resource, software toolkit | Software R package contains various functions for using the data from the Allen Mouse Brain Atlas that is registered to the Common Coordinate Framework. The functionality includes retrieving 3D, CCF aligned, gridded ISH data from the Allen Brain Atlas API, rendering 2D plots of slices of ISH data, retrieving the Mouse Brain Atlas structural ontology, and generating 3D plots of brain structures like those presented in the Allen Brain Explorer. | Allen Mouse Brain Atlas, Common Coordinate Framework, retrieving 3D, CCF aligned, gridded ISH, data, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023817 | COmmon COordinate FRAMEwork in R | 2026-09-19 12:58:27 | 2 | |||||||||
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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 | 2026-09-19 12:58:35 | 2 | |||||
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EyeBrowse Resource Report Resource Website 1+ mentions |
EyeBrowse (RRID:SCR_008000) | data or information resource, data set |
EyeBrowse displays expressed sequence tag (EST) cDNA clones from eye tissues (derived from NEIBank and other sources) aligned with current versions of the human, rhesus, mouse, rat, dog, cow, chicken, or zebrafish genomes, including reference sequences for known genes. This gives a simplified view of gene expression activity from different parts of the eye across the genome. The data can be interrogated in several ways. Specific gene names can be entered into the search window. Alternatively, regions of the genome can be displayed. For example, entering two STS markers separated by a semicolon (e.g. RH18061;RH80175) allows the display of the entire chromosomal region associated with the mapping of a specific disease locus. ESTs for each tissue can then be displayed to help in the selection of candidate genes. In addition, sequences can be entered into a BLAT search and rapidly aligned on the genome, again showing eye derived ESTs for the same region. EyeBrowse includes a custom track display SAGE data for human eye tissues derived from the EyeSAGE project. The track shows the normalized sum of SAGE tag counts from all published eye-related SAGE datasets centered on the position of each identifiable Unigene cluster. This indicates relative activity of each gene locus in eye. Clicking on the vertical count bar for a particular location will bring up a display listing gene details and linking to specific SAGE counts for each eye SAGE library and comparisons with normalized sums for neural and non-neural tissues. To view or alter settings for the EyeSAGE track on EyeBrowse, click on the vertical gray bar at the left of the display. Other custom tracks display known eye disease genes and mapped intervals for candidate loci for retinal disease, cataract, myopia and cornea disease. These link back to further information at NEIBank. For mouse, there is custom track data for ChIP-on-Chip of RNA-Polymerase-II during photoreceptor maturation. |
est, expressed sequence tag, eye, gene, genome, cataract, cdna, chicken, clone, cluster, cornea, cornea disease, cow, data, disease, dog, human, locus, maturation, mouse, myopia, photoreceptor, rat, retina, rhesus, rna polymerase-ii, tag, zebrafish, data analysis software, eye tracking device |
is listed by: 3DVC has parent organization: University of California at Santa Cruz; California; USA |
Retinal disease, Cataract, Myopia, Cornea disease | NEIBank | nif-0000-07733 | SCR_008000 | EyeBrowse | 2026-09-19 12:58:39 | 3 | |||||||
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Phantom Camera Control Resource Report Resource Website 1+ mentions |
Phantom Camera Control (RRID:SCR_021080) | PCC | data analysis software, data processing software, software application, software resource | Software application for Phantom cameras. Controls every camera function on every Phantom camera model. Fine-tune resolution, frame rate, exposure, memory segmentation, trigger modes and automatic functions prior to recording. PCC also makes it easy to work with synchronized cameras, manage Phantom Cine raw files and convert files to format for final project.Software is compatible with Windows 7 Pro and Windows 8.1 and Windows 10, for both 32 and 64-bit operating systems. | Phantom, Phantom camera, image, data, processing, raw files, convert files | Free, Available for download, Freely available | SCR_021080 | 2026-09-19 12:54:48 | 1 | ||||||||||
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Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | data analytics software, data management software, software application, software resource | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html, https://www.sas.com/en_us/software/sas9.html | SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.3, SAS 9.4 | 2026-09-19 12:57:55 | 7485 | ||||||
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STATISTICA Resource Report Resource Website 5000+ mentions |
STATISTICA (RRID:SCR_014213) | data analytics software, software application, software resource | Analytics platform with various sub platforms, each with specific performance capabilities for tasks such as data analysis, data management, data visualization, and data mining procedures. | TIBCO, statistical, test, data, mining, |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Commercially available, Free download available | http://statistica.software.informer.com/10.0/, http://statistica.io/products/ | SCR_014213 | Statistica 10, STATISTICS Product Index, Statistica | 2026-09-19 12:58:11 | 8076 | ||||||||
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elmr Resource Report Resource Website |
elmr (RRID:SCR_017249) | software resource, software toolkit | Software tool as support for working with light and electron microscopy fly brain data. Part of suite of R packages based on NeuroAnatomy Toolbox. Provides tools to move between adult brain EM and light level data, emphasising interaction between CATMAID web application and R Neuroanatomy Toolbox package. | support, working, light, electron, microscopy, fly, brain, data | is related to: NeuroAnatomy Toolbox | Free, Available for download, Freely available | https://jefferis.github.io/elmr/ | SCR_017249 | 2026-09-19 12:58:15 | 0 | |||||||||
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metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software resource, software toolkit | Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis. | sythesis, taxonomy, systematic, review, assemble, screen, literature, extract, meta, data, analysis, statistical |
is listed by: CRAN is related to: R Project for Statistical Computing has parent organization: University of South Carolina; South Carolina; USA |
NSF DBI-1262545; NSF DEB-1451031 |
DOI:10.1111/2041-210X.12472 | Free, Available for download, Freely available | https://github.com/cran/metagear, https://lajeunesse.myweb.usf.edu | SCR_017085 | 2026-09-19 12:58:15 | 0 | |||||||
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-19 12:58:15 | 1908 | ||||||
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Lab Streaming Layer Resource Report Resource Website 50+ mentions |
Lab Streaming Layer (RRID:SCR_017631) | LSL | software application, software resource | System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. | Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG | has parent organization: University of California at San Diego; California; USA | Army Research Laboratory ; NINDS R01 NS047293 |
Free, Freely available | SCR_017631 | Lab Streaming Layer | 2026-09-19 12:58:16 | 86 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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