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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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KinasePhos 3.0 Resource Report Resource Website 1+ mentions |
KinasePhos 3.0 (RRID:SCR_023595) | software resource, software application, simulation software | 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 | 2025-05-12 11:24:06 | 3 | ||||||||
|
Human Protein-Protein Interaction Mining Tool Resource Report Resource Website 1+ mentions |
Human Protein-Protein Interaction Mining Tool (RRID:SCR_008040) | software resource, software application, text-mining software | 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 | 2025-05-12 11:09:46 | 1 | ||||||||
|
Residue Iteration Decomposition Resource Report Resource Website 1+ mentions |
Residue Iteration Decomposition (RRID:SCR_022174) | RIDE | software resource, software toolkit | Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials. | temporal decomposition of EEG signal, EEG, event related potentials, single trial analysis, event related brain potentials, ERP, ERP decomposition method, ERP reconstruction, Latency variability, residue iteration decomposition, single trial analysis | is related to: MATLAB | Hong Kong Baptist University ; Hong Kong Research Grant Council ; National Natural Science Foundation of China ; Germany Hong Kong Joint Research Scheme |
PMID:25455337 | Free, Available for download, Freely available | SCR_022174 | Residue Iteration DEcomposition | 2025-05-12 11:22:37 | 4 | ||||||
|
GetOrganelle Resource Report Resource Website 100+ mentions |
GetOrganelle (RRID:SCR_022963) | software resource, software toolkit | Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes. | Organelle genome assembly, genomic skimming data, organelle genomes, de novo assembly | Chinese Academy of Sciences ; National Natural Science Foundation of China |
PMID:32912315 | Free, Available for download, Freely available | SCR_022963 | 2025-05-12 11:23:27 | 116 | |||||||||
|
SciBet Resource Report Resource Website 1+ mentions |
SciBet (RRID:SCR_024743) | software resource, software application, simulation software | Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells. | supervised cell type identifier, predict cell identity, newly sequenced single cells | National Natural Science Foundation of China | PMID:32286268 | Free, Available for download, Freely available | SCR_024743 | 2025-05-12 11:25:24 | 4 | |||||||||
|
Chinese Genome Sequence Archive Resource Report Resource Website 500+ mentions |
Chinese Genome Sequence Archive (RRID:SCR_025826) | GSE | database, data or information resource | 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 | SCR_025826 | Genome Sequence Archive Family, , Genome Sequence Archive | 2025-05-13 11:20:44 | 545 | ||||||||
|
CancerSEA Resource Report Resource Website 10+ mentions |
CancerSEA (RRID:SCR_026155) | database, data or information resource | 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 | 2025-05-13 11:20:49 | 21 | ||||||||
|
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 | 2025-05-13 11:21:00 | 0 | |||||||
|
PhaSeDis Resource Report Resource Website 1+ mentions |
PhaSeDis (RRID:SCR_024963) | database, data or information resource | Manually curated database of relations between phase separation and diseases. | Manually curated database, relations between phase separation and diseases, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:33126250 | Free, Freely available | SCR_024963 | MloDisDB | 2025-05-13 11:20:19 | 3 | ||||||||
|
PhaSepDB Resource Report Resource Website 10+ mentions |
PhaSepDB (RRID:SCR_024964) | database, data or information resource | 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 | 2025-05-13 11:20:19 | 12 | |||||||||
|
RPS Resource Report Resource Website |
RPS (RRID:SCR_024960) | database, data or information resource | 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 | 2025-05-13 11:20:19 | 0 | |||||||||
|
trRosetta Resource Report Resource Website 50+ mentions |
trRosetta (RRID:SCR_021181) | software resource, software application, simulation software, service 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 | 2025-05-13 11:19:03 | 61 | ||||||
|
DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | service resource, database, data or information resource, storage service resource, data repository | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; State Key Laboratory of Urban Water Resource and Environment ; Scientific Research Fund of Heilongjiang Provincial Education Department |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth https://bio.tools/diseasemeth |
http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2025-05-16 10:57:28 | 31 | ||||
|
funRiceGenes Resource Report Resource Website 10+ mentions |
funRiceGenes (RRID:SCR_015778) | database, data or information resource, data set | Dataset of functionally characterized rice genes and members of different gene families. The dataset was created by integrating data from available databases and reviewing publications of rice functional genomic studies. | rice, functional genomics, interaction network, genetic improvement, gene, data integration | National Key Research and Development Program of China 2016YFD0100903; National Natural Science Foundation of China 31771873 and National Natural Science Foundation of China; Outstanding Young Talents Program |
Freely available, Public, Available for download, Free | https://github.com/venyao/RICENCODE http://funricegenes.ncpgr.cn/ |
SCR_015778 | RICENCODE | 2025-05-16 11:02:26 | 42 | ||||||||
|
m6ASNP: Annotation of genetic variants by m6A function Resource Report Resource Website 1+ mentions |
m6ASNP: Annotation of genetic variants by m6A function (RRID:SCR_016048) | data access protocol, software application, data visualization software, data analysis software, data processing software, web service, software resource | Web server implemented in JAVA and PHP for annotating genetic variants by m6A function. It predicts and annotates N6-methyladenosine (m6A) alterations from genetic variants data such as germline SNPs or cancer somatic mutations. It employs two accurate prediction models for human and mouse using Random Forest algorithm. It conducts a statistical analysis for all the predicted m6A alterations. Provides statistical diagrams and a genome browser to visualize the topology characteristics of predicted m6A alterations. | N6-methyladenosine (m6A), variant annotation, effect prediction, random forest, miclip, m6a, mutant | National Key Research and Development Program 2017YFA0106700; National Natural Science Foundation of China 31771462; China Postdoctoral Science Foundation 2017M622864; Fundamental Research Funds for the Central Universities No. 17lgpy106; Guangdong Natural Science Foundation 2014TQ01R387 |
PMID:29617790 DOI:10.1093/gigascience/giy035 |
Free, Available for download, Freely available | https://github.com/RenLabBioinformatics/m6ASNP | SCR_016048 | m6ASNP | 2025-05-16 11:02:35 | 2 | |||||||
|
CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | data access protocol, database, data or information resource, web service, software 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 | 2025-05-16 11:04:57 | 19 | ||||||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | web service, software resource, 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 | 2025-05-16 11:05:07 | 235 | |||||||||
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Plant mPLoc Resource Report Resource Website 50+ mentions |
Plant mPLoc (RRID:SCR_023014) | web service, software resource, 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 | 2025-05-16 11:05:26 | 79 | ||||||||
|
Gene Expression Profiling Interactive Analysis Resource Report Resource Website 5000+ mentions |
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) | GEPIA | data access protocol, service resource, production service resource, analysis service resource, web service, software 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 | 2025-05-16 11:03:57 | 5025 | ||||||
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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 | 2025-05-16 11:03:53 | 1 |
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