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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 | 2026-02-11 11:00:49 | 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 | 2026-02-11 11:00:49 | 0 | |||||||||
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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 | 2026-02-11 11:01:01 | 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 | 2026-02-11 11:01:07 | 80 | ||||||||
|
PANDA Resource Report Resource Website 100+ mentions |
PANDA (RRID:SCR_002511) | PANDA | software toolkit, software resource | Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface). | analyze, computational neuroscience, connectivity analysis, dicom, format conversion, gnome, linux, macos, matlab, modeling, magnetic resonance, nifti, posix/unix-like, tensor metric, tractography, workflow, xnat pipeline, diffusion mri, chinese, connectome, diffusion metrics, network, pipeline, structural connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National Natural Science Foundation of China ; Beijing Nova Program ; 973 program ; State Key Laboratory of Cognitive Neuroscience and Learning |
PMID:23439846 | Free, Available for download, Freely available | nlx_155911 | http://www.nitrc.org/projects/panda | SCR_002511 | PANDA: a pipeline tool for diffusion MRI, PANDA (Pipeline for Analyzing braiN Diffusion imAges), Pipeline for Analyzing braiN Diffusion imAges, PANDA: Pipeline for Analyzing braiN Diffusion imAges, panda-tool | 2026-02-12 09:43:23 | 376 | ||||
|
CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | data access protocol, software resource, web service, database, data or information resource | Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles. | cancer miRNome interactive analysis, human miRNome data, cancer data, miRNA expression profiles |
is related to: The Cancer Genome Atlas is related to: ArrayExpress |
Riverside Faculty Start-up Fund ; UC Cancer Research Coordinating Committee Competition Award ; UC Academic Senate CoR Research Grant ; United States Department of Agriculture ; National Natural Science Foundation of China ; Science and Technology Project of Guizhou Province |
DOI:10.1093/nar/gkab784 | Free, Freely available | SCR_022092 | 2026-02-12 09:47:57 | 24 | ||||||||
|
Database Commons Resource Report Resource Website 10+ mentions |
Database Commons (RRID:SCR_023661) | data or information resource, database, catalog | Curated catalog of worldwide biological databases to provide landscape of biological databases throughout the world and enable easy retrieval and access to specific collection of databases of interest. Catalog of worldwide biological databases as well as their curated meta information and derived statistics. | Curated catalog, worldwide biological databases, curated meta information, | Strategic Priority Research Program of the Chinese Academy of Sciences ; National Natural Science Foundation of China ; Professional Association of the Alliance of International Science Organizations ; Youth Innovation Promotion Association of Chinese Academy of Sciences ; International Partnership Program of the Chinese Academy of Sciences |
PMID:36572336 PMID:34718731 |
Free, Freely available | SCR_023661 | 2026-02-12 09:48:24 | 13 | |||||||||
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GOEAST - Gene Ontology Enrichment Analysis Software Toolkit Resource Report Resource Website 10+ mentions |
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) | GOEAST | service resource, analysis service resource, production service resource, data analysis service | Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) is a web based software toolkit providing easy to use, visualizable, comprehensive and unbiased Gene Ontology (GO) analysis for high-throughput experimental results, especially for results from microarray hybridization experiments. The main function of GOEAST is to identify significantly enriched GO terms among give lists of genes using accurate statistical methods. Compared with available GO analysis tools, GOEAST has the following unique features: * GOEAST supports analysis for data from various resources, such as expression data obtained using Affymetrix, illumina, Agilent or customized microarray platforms. GOEAST also supports non-microarray based experimental data. The web-based feature makes GOEAST very user friendly; users only have to provide a list of genes in correct formats. * GOEAST provides visualizable analysis results, by generating graphs exhibiting enriched GO terms as well as their relationships in the whole GO hierarchy. * Note that GOEAST generates separate graph for each of the three GO categories, namely biological process, molecular function and cellular component. * GOEAST allows comparison of results from multiple experiments (see Multi-GOEAST tool). The displayed color of each GO term node in graphs generated by Multi-GOEAST is the combination of different colors used in individual GOEAST analysis. Platform: Online tool | statistical analysis, gene ontology, high-throughput, microarray, hybridization, gene, visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Chinese Academy of Sciences; Beijing; China |
National Natural Science Foundation of China 30725014; National Natural Science Foundation of China 90612019; Ministry of Science and Technology of China 2007CB946901; Chinese Academy of Sciences KSCX2-YW-R-134; Chinese Academy of Sciences KSCX2-YW-N-024 |
PMID:18487275 | Free for academic use | biotools:goeast, nlx_149248 | https://bio.tools/goeast | SCR_006580 | Gene Ontology Enrichment Analysis Software Toolkit, Gene Ontology Enrichment Analysis Software Toolkit (GOEAST) | 2026-02-12 09:44:33 | 38 | ||||
|
OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | software resource, web service, data access protocol | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | 2026-02-12 09:47:38 | 255 | |||||||||
|
Plant mPLoc Resource Report Resource Website 100+ mentions |
Plant mPLoc (RRID:SCR_023014) | software resource, web service, data access protocol | Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization. | Predicting Plant Protein Subcellular Localization, predicting subcellular localization, plant proteins, | National Natural Science Foundation of China ; Science and Technology Commission of Shanghai Municipality ; Shanghai Pujiang Program |
PMID:20596258 | Free, Freely available | SCR_023014 | Plant-mPLoc | 2026-02-12 09:47:49 | 105 | ||||||||
|
KinasePhos 3.0 Resource Report Resource Website 1+ mentions |
KinasePhos 3.0 (RRID:SCR_023595) | simulation software, software application, software resource | Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool. | redesign and expansion of prediction, kinase specific phosphorylation sites, kinase specific phosphorylation site prediction, site prediction, kinase specific phosphorylation, | National Natural Science Foundation of China ; Science ; Technology and Innovation Commission of Shenzhen Municipality ; Guangdong Province Basic and Applied Basic Research Fund ; Ganghong Young Scholar Development Fund ; Warshel Institute for Computational Biology |
PMID:35781048 | Free, Available for download, Freely available | https://github.com/tom-209/KinasePhos-3.0-executable-file | SCR_023595 | 2026-02-12 09:47:57 | 3 | ||||||||
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cgmapotools Resource Report Resource Website 1+ mentions |
cgmapotools (RRID:SCR_020950) | software resource, software application, data analysis software, data processing software | Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. | DNA methylomes analysis, DNA methylomes, context-wise analysis, gene-wise analysis, bin-wise analysis, region-wise analysis, sample-wise analysis, bisulfite sequencing data, allele specific methylation detection | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:28968643 | Free, Available for download, Freely available | SCR_020950 | 2026-02-12 09:47:07 | 2 | |||||||||
|
trRosetta Resource Report Resource Website 50+ mentions |
trRosetta (RRID:SCR_021181) | simulation software, service resource, software application, software resource | Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets. | protein structure, restraint-guided structure generation, protein structure prediction | uses: Rosetta | National Natural Science Foundation of China ; Fok Ying-Tong Education Foundation ; Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ; Thousand Youth Talents Plan of China ; China Scholarship Council ; NIGMS R01 GM092802; NIH Office of the Director DP5 OD026389 |
PMID:31896580 | Free, Freely available | https://github.com/gjoni/trRosetta | SCR_021181 | transformed restrained Rosetta | 2026-02-12 09:47:15 | 67 | ||||||
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CIRIquant Resource Report Resource Website 1+ mentions |
CIRIquant (RRID:SCR_021661) | software toolkit, software resource, software application, data analysis software, data processing software | Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. | circRNA quantification, differential expression analysis, RNA-Seq data, circular RNA, circular isoform switching events | National Natural Science Foundation of China | DOI:10.1038/s41467-019-13840-9 | Free, Available for download, Freely available | https://sourceforge.net/projects/ciri/files/ https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_0_home.html# |
SCR_021661 | 2026-02-12 09:47:15 | 1 | ||||||||
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CIRCexplorer2 Resource Report Resource Website 10+ mentions |
CIRCexplorer2 (RRID:SCR_021664) | software resource, software application, data analysis software, data processing software | Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs. | Decipher alternative back splicing, decifer circRNAs splicing pattern, circular RNA analysis, annotate circRNAs | National Natural Science Foundation of China ; Ministry of Science and Technology of China |
PMID:27365365 PMID:30539552 |
Free, Available for download, Freely available | SCR_021664 | 2026-02-12 09:47:24 | 40 | |||||||||
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Gene Expression Profiling Interactive Analysis Resource Report Resource Website 5000+ mentions |
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) | GEPIA | analysis service resource, data access protocol, software resource, service resource, web service, production service resource | Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis. | Cancer gene expression, normal gene expression, analysis, RNA sequencing, expression data, TCGA project, GTEx project, patient survival analysis, correlation analysis |
is related to: Gene Expression Profiling Interactive Analysis 2 has parent organization: Peking University; Beijing; China |
Cancer | Peking University ; National Natural Science Foundation of China |
PMID:28407145 | Free, Freely available | SCR_018294 | 2026-02-12 09:46:49 | 5635 | ||||||
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GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | data access protocol, software resource, service resource, web service, data or information resource, portal | Web service for prediction of SUMOylation sites and SUMO-interaction motifs in proteins by CUCKOO Workgroup. | Small ubiquitin like modifier, SUMOs, sumoylation, covalently modified protein, group prediction system, site prediction, interaction motif in protein, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China ; National Basic Research Program ; Guangdong Natural Science Funds for Distinguished Young Scholar ; Zhujiang Nova Program of Guangzhou ; International Science and Technology Cooperation Program of China |
PMID:24880689 | Restricted | biotools:gps-sumo | http://sumosp.biocuckoo.org/online.php https://bio.tools/gps-sumo |
SCR_018261 | Group-based Prediction System -Small Ubiquitin-like MOdifiers, Small Ubiquitin-like MOdifiers sp, GPS-SUMO 2.0, SUMOsp, GPS Small Ubiquitin-like MOdifiers, Group-based Prediction System-SUMO | 2026-02-12 09:47:01 | 2 | |||||
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TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | analysis service resource, software resource, data access protocol, service resource, web service, production service resource | Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features. | Tumor, tumor infiltrating immune cell, immune cell, cell, analysis, cancer cell, cancer type, tumor immunological feature, tumor genomic feature, display | National Natural Science Foundation of China ; NCI CA180980; Dana-Farber Cancer Institute |
PMID:29092952 | Free, Freely available | SCR_018737 | Tumor IMmune Estimation Resource | 2026-02-12 09:47:05 | 2042 | |||||||
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SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2026-02-12 09:47:00 | 1 | |||||||
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Human Protein-Protein Interaction Mining Tool Resource Report Resource Website 1+ mentions |
Human Protein-Protein Interaction Mining Tool (RRID:SCR_008040) | text-mining software, software application, software resource | Web-based tool used to mine human protein-protein interactions (PPIs) from PubMed abstracts based on their co-occurrences and interaction words, followed by evidencs in human PPI databases and shared terms in GO database. | protein-protein interaction, pubmed, text mining |
is listed by: 3DVC has parent organization: Chinese Academy of Sciences; Beijing; China |
Hi-Tech Research and Development Program of China 2006AA02Z322; National Natural Science Foundation of China 30525007; National Natural Science Foundation of China 30730049; National Basic Research Program of China 2006CB504100; National Basic Research Program of China 2006CB500700; National Basic Research Program of China 2007CB947200 |
nif-0000-10256 | SCR_008040 | PPI Finder | 2026-02-12 09:44:35 | 1 |
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