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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SOAPBarcode Resource Report Resource Website 100+ mentions |
SOAPBarcode (RRID:SCR_015776) | sequencing analysis software | Software for metabarcoding of DNA. SOAPBarcode takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms and can characterize the biodiversity of large volumes of eukaryote samples. | metabarcoding, metabarcode, bgi, soap, ngs, next generation sequencing, eukaryote | National High-tech Research and Development Project (863) of China 2012AA021601; Yunnan Province 20080A001; Chinese Academy of Sciences 0902281081; Chinese Academy of Sciences KSCX2-YW-Z-1027; National Natural Science Foundation of China 31170498; Ministry of Science and Technology of China 2012FY110800; University of East Anglia |
Free, Available for download | SCR_015776 | metabarcoding | 2026-08-29 11:25:01 | 221 | |||||||||
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Resting State Hemodynamic Response Function Retrieval and Deconvolution Resource Report Resource Website 1+ mentions |
Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) | rsHRF | software resource, software toolkit | Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images. | hemodynamic response function, HRF estimation and deconvolution, resting state BOLD signal, GIfTI images, NIfTI images, brain | European Union Horizon 2020 Framework Programme ; Fund for Scientific Research-Flanders ; National Natural Science Foundation of China |
PMID:34560269 | Free, Available for download, Freely available | https://github.com/compneuro-da/rsHRF | SCR_023663 | 2026-08-29 11:31:30 | 4 | |||||||
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Beijing: Eyes Open Eyes Closed Study Resource Report Resource Website |
Beijing: Eyes Open Eyes Closed Study (RRID:SCR_001507) | Beijing EOEC | data or information resource, data set | Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed. | early adult human, resting state, fmri, diffusion tensor imaging, resting state fmri, eyes open, eyes closed, neuroimaging, mprage, image collection, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China (863) 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_152810 | SCR_001507 | Beijing Eyes Open Eyes Closed Study, Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Eyes Open Eyes Closed Sample, Eyes Open Eyes Closed Sample, BNU Eyes Open Eyes Closed Sample | 2026-08-29 11:31:47 | 0 | |||||
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iNPS Resource Report Resource Website 10+ mentions |
iNPS (RRID:SCR_015750) | algorithm resource, software resource | Software for nucleosome detection that builds on the NPS software. Its application to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nucleosome, detection, nps, sequencing data, nucleosome positioning | is related to: NPS | Chinese Academy of Sciences KSCX2-EW-J-15; Chinese Academy of Sciences KSCX2-EW-R-02; Chinese Academy of Sciences YZ201243; Chinese Ministry of Science and Technology 2011CB504206; Fundamental Research Funds for the Central Universities 2014JBZ005; National Natural Science Foundation of China 31210103916; National Natural Science Foundation of China 91019019; Shanghai Academic Leader Project 11XD1405700; Stem Cell Leading Project XDA01010303 |
PMID:25233085 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015750 | iNPS: An improved algorithm for accurate nucleosome positioning from sequencing data | 2026-08-29 11:31:19 | 25 | |||||||
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shinyCircoss Resource Report Resource Website 1+ mentions |
shinyCircoss (RRID:SCR_022367) | software application, software resource | Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively. | Circos plot, interactive creation |
uses: Shiny uses: R Project for Statistical Computing is related to: RCircos is related to: RStudio is related to: CRAN |
Fundamental Research Funds for the Central Universities ; National Key Research and Development Program of China ; National Natural Science Foundation of China ; National Program for Support of Top-notch Young Professionals |
PMID:29186362 | Free, Available for download, Freely available | https://github.com/YaoLab-Bioinfo/shinyCircos | SCR_022367 | 2026-08-29 11:31:29 | 3 | |||||||
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HDOCK server Resource Report Resource Website 500+ mentions |
HDOCK server (RRID:SCR_024799) | data access protocol, software resource, web service | Web server for protein-protein and protein-DNA/RNA docking based on hybrid strategy. With input information for receptor and ligand molecules either amino acid sequences or Protein Data Bank structures, the server automatically predicts their interaction through hybrid algorithm of template-based and template-free docking. | Web server, protein-protein docking, protein-DNA/RNA docking, amino acid sequences, Protein Data Bank structures, receptor and ligand molecules input information, interaction prediction, | Huazhong University of Science and Technology ; National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:28521030 PMID:32269383 |
Free, Freely available | SCR_024799 | HDOCK | 2026-08-29 11:33:44 | 566 | ||||||||
|
LLPSDB Resource Report Resource Website 1+ mentions |
LLPSDB (RRID:SCR_024966) | data or information resource, database | Database of proteins undergoing liquid–liquid phase separation in vitro. Contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments. | proteins, liquid–liquid phase separation in vitro, LLPS, Liquid Liquid Phase Separation related proteins, | National Natural Science Foundation of China | DOI:10.1093/nar/gkz778 | Free, Freely available | SCR_024966 | Liquid Liquid Phase Separation DataBase | 2026-08-29 11:33:51 | 4 | ||||||||
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PhaSePred Resource Report Resource Website 10+ mentions |
PhaSePred (RRID:SCR_024969) | data access protocol, software resource, web service | Web server as meta-predictor for phase-separating proteins. Displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins. | meta-predictor for phase-separating proteins, proteome-level quantiles of different features, profiling PS propensity, | Clinical Medicine Plus X-Young Scholars Project of Peking University ; Fundamental Research Funds for the Central Universities ; National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:35687670 | Free, Freely available | SCR_024969 | 2026-08-29 11:33:51 | 16 | |||||||||
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RNAPhaSep Resource Report Resource Website |
RNAPhaSep (RRID:SCR_024958) | data or information resource, database | Database that collects phase separation related RNAs manually curated from publication and public databases. | phase separation related RNAs, publication and public databases data collection, manually curated, | China Postdoctoral Science Foundation ; Fujian Medical University Research Foundation of Talented Scholars ; Guangdong Basic and Applied Basic Research Foundation ; National Key Research and Development Project of China ; National Natural Science Foundation of China |
PMID:34718740 | Free, Freely available | SCR_024958 | 2026-08-29 11:33:50 | 0 | |||||||||
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quarTeT Resource Report Resource Website 10+ mentions |
quarTeT (RRID:SCR_025258) | software resource, source code, web application | Web toolkit for studies of large scale T2T genomes. Collection of tools designed for T2T genome assembly and characterization, including reference guided genome assembly, ultra long sequence based gap filling, telomere identification, and de novo centromere prediction. Includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. Modules can be used alone or in combination with each other for T2T genome assembly and characterization. | Telomere-To-Telomere genomes studies, guided genome assembly, ultra long sequence based gap filling, telomere identification, de novo centromere prediction, large scale T2T genomes, assemble and analyse multiple high quality genomes, highly repetitive regions in genomes, | National Natural Science Foundation of China | PMID:37560017 | Free, Available for download, Freely available | https://github.com/aaranyue/quarTeT | SCR_025258 | quar Telomere-To-Telomere Toolkit | 2026-08-29 11:33:59 | 41 | |||||||
|
NECAT Resource Report Resource Website 10+ mentions |
NECAT (RRID:SCR_025350) | data analysis software, data processing software, software application, software resource, source code | Software error correction and de-novo assembly tool for Nanopore long noisy reads. Nanopore data assembler. | Nanopore, data assembler, Nanopore long noisy reads, de-novo assembly, error correction, | Guangdong Basic and Applied Basic Research Foundation ; National Natural Science Foundation of China ; US National Institute of Food and Agriculture ; US National Science Foundation |
PMID:33397900 | Free, Available for download, Freely available | SCR_025350 | 2026-08-29 11:33:54 | 27 | |||||||||
|
uAI Research Portal Resource Report Resource Website 1+ mentions |
uAI Research Portal (RRID:SCR_025870) | data or information resource, portal, software resource | AI-powered integrated research platform for one-stop analysis of medical images. Provides advanced functionality such as automatic segmentation, registration, and classification for variety of application domains. Has major merits including Advanced built-in algorithms applicable to multiple imaging modalities (i.e., CT, MR, PET, DR), diseases (i.e., tumor, neurodegenerative disease, pneumonia), and applications (i.e., diagnosis, treatment planning, follow-up); Iterative deep learning-based training strategy for fast delineation of ROIs of large-scale datasets, thereby saving clinicians' time and obtaining novel and more robust models; Modular architecture with customization and extensibility, where plugins can be designed for specific purposes. | United Imaging Intelligence Inc, medical images, clinical big data management, intelligent data annotation, 3D image rendering, radiomics analysis, deep learning model training, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:37492386 | Restricted | SCR_025870 | United Imaging Intelligence uAI Research Portal | 2026-08-29 11:34:33 | 2 | ||||||||
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Spatial DB Resource Report Resource Website 10+ mentions |
Spatial DB (RRID:SCR_026135) | data or information resource, database | Database for spatially resolved transcriptomes. Provides curated spatially resolved transcriptomic data from published papers, aiming to provide comprehensive and accurate resource of spatial gene expression profiles in tissues. Allows users to browse spatial gene expression profile and compare spatial gene expression profile of any two datasets generated by same or different techniques side by side. | Spatially resolved transcriptomics, gene expression profiles, positional information, disease pathology, spatial gene expression profiles in tissues, curated data, | National Natural Science Foundation of China | PMID:31713629 | Free, Freely available | SCR_026135 | 2026-08-29 11:34:20 | 16 | |||||||||
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CB-dock2 Resource Report Resource Website 100+ mentions |
CB-dock2 (RRID:SCR_026134) | data access protocol, software resource, web service | Web server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting. Given the three-dimensional structure of protein and ligand, can predict their binding sites and affinity for computer-aided drug discovery. | protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting, predict binding sites, drug discovery, | National Natural Science Foundation of China | PMID:35609983 | Free, Freely available | SCR_026134 | 2026-08-29 11:34:37 | 170 | |||||||||
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HERB Resource Report Resource Website 100+ mentions |
HERB (RRID:SCR_026468) | data or information resource, database | High-throughput experiment- and reference-guided database of traditional Chinese medicine. | traditional Chinese medicine, experiment- and reference-guided database, | China Postdoctoral Innovative Talent Foundation ; National Natural Science Foundation of China ; Zhejiang Provincial Natural Science Foundation of China |
PMID:33264402 | Free, Freely available, | SCR_026468 | 2026-08-29 11:34:31 | 284 | |||||||||
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ROGUE Resource Report Resource Website 1+ mentions |
ROGUE (RRID:SCR_026568) | data analysis software, data processing software, software application, software resource, source code | Software tool as entropy-based metric for assessing purity of single cell populations. Used to accurately quantify purity of identified cell clusters. | Assessing purity of single cell population, entropy-based metric, quantify purity, identified cell clusters, | National Natural Science Foundation of China ; Peking University |
PMID:32572028 | Free, Available for download, Freely available | SCR_026568 | 2026-08-29 11:34:34 | 3 | |||||||||
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FerrDb Resource Report Resource Website 100+ mentions |
FerrDb (RRID:SCR_026852) | data or information resource, database | Manually curated database of ferroptosis regulators and ferroptosis-disease associations. There are two secondary categories of ferroptosis regulators: (1) genes and (2) substances. Gene regulators include driver, suppressor, marker, and unclassified regulator. Substances cover range of chemical entities, including pure substances (e.g., iron, erastin) and mixtures (e.g., herbal extracts). Substance regulators include inducers and inhibitors. FerrDb V2 is updated database. | Manually curated database, ferroptosis regulators, ferroptosis-disease associations, | Guangzhou Municipal Key Discipline in Medicin ; Guangzhou Municipal Psychiatric Disease Clinical Transformation Laboratory ; National Natural Science Foundation of China |
PMID:36305834 PMID:32219413 |
Free, Freely available | SCR_026852 | FerrDb V2 | 2026-08-29 11:34:51 | 200 | ||||||||
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DOSE Resource Report Resource Website 10+ mentions |
DOSE (RRID:SCR_027408) | DOSE | software resource, software toolkit | Software R package for disease ontology semantic and enrichment analysis. | disease ontology, semantic and enrichment analysis, | National Natural Science Foundation of China | PMID:25677125 | Free, Available for download, Freely available | SCR_027408 | Disease Ontology Semantic and Enrichment, Disease Ontology Semantic and Enrichment (DOSE) | 2026-08-29 11:35:06 | 12 | |||||||
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CSOmap Resource Report Resource Website 1+ mentions |
CSOmap (RRID:SCR_027636) | software application, software resource, source code | Software tool for reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Infers cellular spatial organization from scRNA-seq by modeling ligand–receptor-mediated self-assembly. It constructs 3D pseudo-space and quantifies cell–cell interactions for downstream visualization and hypothesis testing. | Infer cellular spatial organization from scRNA-seq, modeling ligand–receptor-mediated self-assembly, reconstruction of cell spatial organization, single-cell RNA sequencing data, construct 3D pseudo-space, quantify cell–cell interactions, | National Natural Science Foundation of China ; Peking University |
PMID:32541867 | Free, Available for download, Freely available | SCR_027636 | 2026-08-29 11:35:10 | 1 | |||||||||
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Cancer Treatment Response gene signature DataBase Resource Report Resource Website 1+ mentions |
Cancer Treatment Response gene signature DataBase (RRID:SCR_027950) | CTR_DB | data or information resource, database | Data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. CTR-DB 2.0 is updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers. | clinical transcriptomes, cancer treatment response, primary drug resistance, predictive biomarkers, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:39494527 | Free, Freely available, | SCR_027950 | , CTR-DB 1.0, CTR-DB 2.0 | 2026-08-29 11:35:17 | 5 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
