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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TAM Resource Report Resource Website 1+ mentions |
TAM (RRID:SCR_023800) | data access protocol, software resource, web service | Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis. | miRNA set enrichment analysis, functional and disease annotations testing, miRNAs, overrepresentation analysis, | National Natural Science Foundation of China ; Fundamental Research Funds for Central Universities of China ; Natural Science Foundation of Hebei Province ; Doctoral Fund of Ministry of Education of China |
PMID:29878154 PMID:20696049 |
Free, Freely available | SCR_023800 | TAM 2.0 | 2026-02-13 10:59:03 | 2 | ||||||||
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miRBaseConverter Resource Report Resource Website 1+ mentions |
miRBaseConverter (RRID:SCR_023873) | data analysis software, software resource, data processing software, software application | Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends. | converting and retrieving miRNAs information, miRNAs information, different miRBase versions, miRNA Name, miRNA Accession, miRNA Sequence, miRNA Version, miRNA History, miRNA Family, miRNA | Australian Research Council Discovery Project ; National Health and Medical Research council ; Presidential Foundation of Hefei Institutes of Physical Science ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; Applied Basic Research Foundation of Science and Technology of Yunnan Province ; Shanghai Key Laboratory of Intelligent Information Processing China |
PMID:30598108 | Free, Available for download, Freely available | https://github.com/taoshengxu/miRBaseConverter | SCR_023873 | 2026-02-13 10:59:02 | 3 | ||||||||
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RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/ http://www.rnalocate.org/ |
SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-02-13 10:59:15 | 12 | ||||||
|
PopLDdecay Resource Report Resource Website 100+ mentions |
PopLDdecay (RRID:SCR_022509) | data analysis software, software resource, data processing software, software application | Software tool for linkage disequilibrium decay analysis based on variant call format files. | linkage disequilibrium decay analysis, variant call format, VCF) files | National Natural Science Foundation of China ; China Postdoctoral Science Foundation |
PMID:30321304 | Free, Available for download, Freely available | SCR_022509 | 2026-02-13 10:58:44 | 117 | |||||||||
|
PharmMapper Resource Report Resource Website 50+ mentions |
PharmMapper (RRID:SCR_022604) | data access protocol, software resource, web service | Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database. | potential drug target identification, given probe small molecules, identify potential target candidates, binding targets unidentified, pharmacophore mapping approach, drug target identification, target pharmacophore database | National Natural Science Foundation of China ; Shanghai Committee of Science and Technology ; Major National Scientific and Technological Project of China |
PMID:20430828 PMID:28472422 |
Free, Freely available | SCR_022604 | PharmMapper 2017 | 2026-02-13 10:58:45 | 97 | ||||||||
|
IPEV Resource Report Resource Website 1+ mentions |
IPEV (RRID:SCR_023702) | data analysis software, software resource, data processing software, software application | Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences. | Prokaryotic and Eukaryotic virus derived sequences, identify sequences, virome, eukaryotic viral sequences, prokaryotic viral sequences, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
DOI:10.1101/2023.05.28.541705 | Free, Available for download, Freely available | SCR_023702 | Identification of Prokaryotic and Eukaryotic Virus | 2026-02-13 10:59:04 | 1 | ||||||||
|
HDOCK server Resource Report Resource Website 100+ 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, | National Natural Science Foundation of China ; Huazhong University of Science and Technology ; National Key Research and Development Program of China |
PMID:28521030 PMID:32269383 |
Free, Freely available | SCR_024799 | HDOCK | 2026-02-13 10:59:18 | 304 | ||||||||
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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, | National Key Research and Development Program of China ; National Natural Science Foundation of China ; Clinical Medicine Plus X-Young Scholars Project of Peking University ; Fundamental Research Funds for the Central Universities |
PMID:35687670 | Free, Freely available | SCR_024969 | 2026-02-13 10:59:19 | 10 | |||||||||
|
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 | 2026-02-13 10:59:24 | 33 | |||||||
|
NECAT Resource Report Resource Website 10+ mentions |
NECAT (RRID:SCR_025350) | data processing software, data analysis software, source code, software application, software resource | 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, | National Natural Science Foundation of China ; Guangdong Basic and Applied Basic Research Foundation ; US National Institute of Food and Agriculture ; US National Science Foundation |
PMID:33397900 | Free, Available for download, Freely available | SCR_025350 | 2026-02-13 10:59:33 | 13 | |||||||||
|
ROGUE Resource Report Resource Website 1+ mentions |
ROGUE (RRID:SCR_026568) | data processing software, data analysis software, source code, software application, software resource | 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, | Peking University ; National Natural Science Foundation of China |
PMID:32572028 | Free, Available for download, Freely available | SCR_026568 | 2026-02-13 10:59:42 | 1 | |||||||||
|
uAI Research Portal Resource Report Resource Website 1+ mentions |
uAI Research Portal (RRID:SCR_025870) | data or information resource, software resource, portal | 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 | 2026-02-13 10:59:41 | 1 | ||||||||
|
CB-dock2 Resource Report Resource Website 50+ 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 | 2026-02-13 10:59:42 | 55 | |||||||||
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DOSE Resource Report Resource Website 1+ 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) | 2026-02-13 10:59:56 | 8 | |||||||
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CSOmap Resource Report Resource Website 1+ mentions |
CSOmap (RRID:SCR_027636) | software resource, source code, software application | 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, | Peking University ; National Natural Science Foundation of China |
PMID:32541867 | Free, Available for download, Freely available | SCR_027636 | 2026-02-13 11:00:00 | 1 | |||||||||
|
shinyCircoss Resource Report Resource Website 1+ mentions |
shinyCircoss (RRID:SCR_022367) | software resource, software application | 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 |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; National Program for Support of Top-notch Young Professionals ; Fundamental Research Funds for the Central Universities |
PMID:29186362 | Free, Available for download, Freely available | https://github.com/YaoLab-Bioinfo/shinyCircos | SCR_022367 | 2026-02-13 10:58:42 | 2 | |||||||
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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 | National Natural Science Foundation of China ; Fund for Scientific Research-Flanders ; European Union Horizon 2020 Framework Programme |
PMID:34560269 | Free, Available for download, Freely available | https://github.com/compneuro-da/rsHRF | SCR_023663 | 2026-02-13 10:59:00 | 3 |
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