Searching the RRID Resource Information Network
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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PhaSepDB Resource Report Resource Website 10+ mentions |
PhaSepDB (RRID:SCR_024964) | data or information resource, database | Provides a collection of manually curated phase separation (PS) proteins and Membraneless organelles (MLOs) related proteins. Annotated phase separation-related proteins with droplet states, co-phase separation partners and other experimental information. | Membraneless organelles related proteins, collection of manually curated phase separation proteins, phase separation proteins, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
DOI:10.1093/nar/gkac783 | Free, Freely available | SCR_024964 | 2026-02-14 02:08:59 | 20 | |||||||||
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RPS Resource Report Resource Website |
RPS (RRID:SCR_024960) | data or information resource, database | Comprehensive database of RNAs involved in liquid-liquid phase separation. | RNAs, liquid-liquid phase separation, | National Natural Science Foundation of China ; Program for Guangdong Introducing Innovative and Entrepreneurial Teams ; Guangdong Basic and Applied Basic Research Foundation |
PMID:34718734 | Free, Freely available | SCR_024960 | 2026-02-14 02:08:59 | 0 | |||||||||
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IOBR Resource Report Resource Website 10+ mentions |
IOBR (RRID:SCR_025619) | data analysis software, software resource, data processing software, software application | Software R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. Used for comprehensively interpreting multi-omics data. | interpreting multi-omics data, perform comprehensive analysis, | National Natural Science Foundation of China ; Guangzhou Planned Project of Science and Technology |
PMID:34276676 | Free, Available for download, Freely available, | SCR_025619 | Immuno-Oncology Biological Research | 2026-02-14 02:08:48 | 29 | ||||||||
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hTFtarget Resource Report Resource Website 10+ mentions |
hTFtarget (RRID:SCR_025626) | data or information resource, software resource, source code, database | Comprehensive database for regulations of Human Transcription Factors and their targets. Provides tools for visualization, interpretation, and analysis of pathway knowledge. | Human transcription factor database, human transcription factor, pathway knowledge, | National Natural Science Foundation of China ; National Key R&D Program of China ; China Postdoctoral Science Foundation |
PMID:32858223 | Free, Freely available | http://bioinfo.life.hust.edu.cn/hTFtarget | SCR_025626 | 2026-02-14 02:09:05 | 40 | ||||||||
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stMMR Resource Report Resource Website 1+ mentions |
stMMR (RRID:SCR_025601) | software resource, source code, software application | Software tool for spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation. | spatial domain identification, spatially resolved transcriptomics, multi-modal feature representation, | National Natural Science Foundation of China ; Natural Science Foundation of Shandong Province |
DOI:10.1101/2024.02.22.581503 | Free, Available for download, Freely available, | SCR_025601 | 2026-02-14 02:09:04 | 1 | |||||||||
|
Chinese Genome Sequence Archive Resource Report Resource Website 1000+ mentions |
Chinese Genome Sequence Archive (RRID:SCR_025826) | GSE | data or information resource, database | Public archive of raw sequence data in National Genomics Data Center as part of the China National Center for Bioinformation. GSA accepts worldwide data submissions, performs data curation and quality control for all submitted data. Provides data storage and sharing services. | Chinese National Genomics Data Center, raw sequence data, data storage and sharing, | National Key R and D Program of China ; Strategic Priority Research Program of Chinese Academy of Sciences ; Genomics Data Center Construction of Chinese Academy of Sciences ; National Natural Science Foundation of China ; International Partnership Program of the Chinese Academy of Sciences |
PMID:34400360 | r3d100012342 | https://doi.org/10.17616/R3094D | SCR_025826 | Genome Sequence Archive Family, , Genome Sequence Archive | 2026-02-14 02:08:52 | 1031 | ||||||
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CancerSEA Resource Report Resource Website 50+ mentions |
CancerSEA (RRID:SCR_026155) | data or information resource, database | Database that aims to comprehensively explore distinct functional states of cancer cells at the single-cell level. Provides functional state-associated PCG/lncRNA repertoires across all cancers, in specific cancers, and in individual cancer single-cell datasets. Provides interface for comprehensively searching, browsing, visualizing and downloading functional state activity profiles of cancer single cells and corresponding PCGs/lncRNAs expression profiles. | cancer single cells, PCGs/lncRNAs expression profiles, distinct functional states of cancer cells, single-cell level, searching, browsing, visualizing and downloading, functional state activity profiles, | National High Technology Research and Development Program of China ; National Natural Science Foundation of China |
PMID:30329142 | Free, Freely available | SCR_026155 | Cancer Single-cell State Atlas | 2026-02-14 02:09:34 | 80 | ||||||||
|
Gene Expression Profiling Interactive Analysis 2 Resource Report Resource Website 500+ mentions |
Gene Expression Profiling Interactive Analysis 2 (RRID:SCR_026154) | data access protocol, software resource, web service | Enhanced web server for large-scale expression profiling and interactive analysis. GEPIA2 is updated and enhanced version of GEPIA, offering more functionalities, higher resolution data analysis, and additional features like ability to analyze specific cancer subtypes, quantify gene signatures based on single-cell sequencing studies, and allow users to upload their own RNA-seq data for comparison with the TCGA and GTEx datasets; essentially providing more comprehensive and advanced platform for gene expression analysis compared to the original GEPIA version. | gene expression analysis, large-scale expression profiling, interactive analysis, quantify gene signatures, | is related to: Gene Expression Profiling Interactive Analysis | National Natural Science Foundation of China ; Peking University |
PMID:31114875 | Free, Freely available | GEPIA2 | http://gepia2.cancer-pku.cn/ | SCR_026154 | Gene Expression Profiling Interactive Analysis 2 | 2026-02-14 02:09:10 | 545 | |||||
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HapHiC Resource Report Resource Website 10+ mentions |
HapHiC (RRID:SCR_026284) | software resource, source code, software application | Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules. | reference-independent, allele-aware scaffolding tool, performance on chromosome assignment, contig ordering and orientation, Hi-C data, scaffold haplotype-phased genome assemblies, chromosome-scale pseudomolecules, | National Natural Science Foundation of China | PMID:39103456 | Free, Available for download, Freely available | SCR_026284 | 2026-02-14 02:09:12 | 13 | |||||||||
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Coding-Non-Coding Index Resource Report Resource Website |
Coding-Non-Coding Index (RRID:SCR_026554) | CNCI | software resource, source code, software application | Software tool for utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. | utilizing sequence intrinsic composition, classify protein-coding and long non-coding transcripts, | National Natural Science Foundation of China | PMID:23892401 | Free, Available for download, Freely available | SCR_026554 | Coding-Non-Coding Index (CNCI) | 2026-02-14 02:09:16 | 0 | |||||||
|
STPoseNet Resource Report Resource Website |
STPoseNet (RRID:SCR_026834) | software resource, source code | Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation. | OpenBehavior, spatiotemporal network model, mouse pose estimation, | is listed by: OpenBehavior | National Natural Science Foundation of China | PMID:38711440 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/stposenet/ | SCR_026834 | 2026-02-14 02:09:48 | 0 | |||||||
|
SemiBin Resource Report Resource Website 10+ mentions |
SemiBin (RRID:SCR_026896) | software resource, source code, software application | Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning. | command tool, metagenomic binning, contig level, short and long reads, | National Natural Science Foundation of China ; Shanghai Municipal Science and Technology Major Project |
PMID:35484115 PMID:37387171 |
Free, Available for download, Freely available | SCR_026896 | SemiBin2 | 2026-02-14 02:09:49 | 10 | ||||||||
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ggVennDiagram Resource Report Resource Website 10+ mentions |
ggVennDiagram (RRID:SCR_026950) | software resource, source code, software toolkit | Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram. | generate Venn diagram, | uses: ggplot2 | National Natural Science Foundation of China ; Royal Society-Newton Advanced Fellowship ; National Key Research Program of China ; Wuhan Applied Foundational Frontier Project ; Fundamental Research Funds for the Central Universities |
PMID:34557218 | Free, Available for download, Freely available | https://github.com/gaospecial/ggVennDiagram | SCR_026950 | 2026-02-14 02:09:51 | 37 | |||||||
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GFFx Resource Report Resource Website 1+ mentions |
GFFx (RRID:SCR_027445) | software resource, source code, software toolkit | Software Rust-Based suite of utilities for ultra-fast genomic feature extraction. Used for ultra-fast and scalable genome annotation access. Can be used both as a command-line tool and as a Rust library. | genomic feature extraction, genome annotation access, | National Natural Science Foundation of China | DOI:10.1101/2025.08.08.669426 | Free, Available for download, Freely available | https://crates.io/crates/gffx | SCR_027445 | 2026-02-14 02:09:23 | 1 | ||||||||
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SeedGerm-VIG Resource Report Resource Website 1+ mentions |
SeedGerm-VIG (RRID:SCR_027483) | data processing software, data analysis software, source code, time-series analysis software, software application, software resource | Software pipeline to quantify seed vigour in wheat and other cereal crops using deep learning powered dynamic phenotypic analysis. | seed vigour, germination, vision-based deep learning, dynamic trait analysis, wheat | National Natural Science Foundation of China 32070400 & U24A20402; Allan & Gill Gray Foundation’ Sustainable Productivity for Crop Improvement G118688; the United Kingdom Research and Innovation's (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) AI in Bioscience Grant BB/Y513969/1; BBSRC’s International Partnership Grant BB/Y514081/1; BBSRC’s ALERT grant BB/X019683/1 |
DOI:10.1093/gigascience/giaf129 | Free, Available for download, Freely available | SCR_027483 | 2026-02-14 02:09:31 | 1 | |||||||||
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ImmuCellAI Resource Report Resource Website 1+ mentions |
ImmuCellAI (RRID:SCR_027645) | software resource, source code, software application | Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy. | Cell subsets abundance prediction, predicting immunotherapy response, cancer immunotherapy estimate, immune cells, gene expression dataset, | National Natural Science Foundation of China | PMID:32274301 | Free, Available for download, Freely available | https://github.com/lydiaMyr/ImmuCellAI | SCR_027645 | Immune Cell Abundance Identifier | 2026-02-14 02:09:27 | 6 | |||||||
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | data or information resource, experimental protocol, narrative resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/ https://bio.tools/int_hapmap_project https://doi.org/10.17616/R3H06Q |
http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-02-14 02:00:33 | 6817 | |||
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Consortium for Reliability and Reproducibility Resource Report Resource Website 1+ mentions |
Consortium for Reliability and Reproducibility (RRID:SCR_003774) | CoRR | data or information resource, portal, data set | Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans | consortium, connectomics, reproducibility, resting state fmri, fmri, diffusion mri, neuroimaging, metadata standard, functional image, dti, anatomical image, functional, anatomical |
uses: Mind Research Network - COINS uses: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project |
NIDA ; National Natural Science Foundation of China ; Child Mind Institute ; Institute of Psychology ; Chinese Academy of Sciences ; Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Registration required, (NITRC), Open unspecified license | nlx_158048 | SCR_003774 | Consortium for Reliability and Reproducibility (CoRR) | 2026-02-14 02:00:53 | 6 | ||||||
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Arabidopsis Hormone Database Resource Report Resource Website 10+ mentions |
Arabidopsis Hormone Database (RRID:SCR_001792) | AHD, AHD2.0 | ontology, data repository, storage service resource, data or information resource, service resource, controlled vocabulary, database | Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions. | arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis service |
is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 30625003; National Natural Science Foundation of China 30730011; Ministry of Science and Technology of China 2009CB119101; Ministry of Education of China ED20060047 |
PMID:21045062 PMID:19015126 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02559 | SCR_001792 | Arabidopsis Hormone Database 2.0 | 2026-02-14 02:00:18 | 28 | |||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | data repository, storage service resource, data or information resource, service resource, database | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-02-14 02:00:14 | 8 |
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