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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
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 2026-02-10 09:55:44 1
KinasePhos 3.0
 
Resource Report
Resource Website
1+ mentions
KinasePhos 3.0 (RRID:SCR_023595) simulation software, software resource, software application 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 2026-02-10 09:58:38 3
SnpHub
 
Resource Report
Resource Website
1+ mentions
SnpHub (RRID:SCR_018177) web application, software resource 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 2026-02-10 09:57:38 1
DiseaseMeth
 
Resource Report
Resource Website
10+ mentions
DiseaseMeth (RRID:SCR_005942) data repository, data or information resource, database, service resource, storage service resource 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 2026-02-11 10:57:12 34
SpliceDisease
 
Resource Report
Resource Website
1+ mentions
SpliceDisease (RRID:SCR_006130) SpliceDisease data repository, data or information resource, database, service resource, storage service resource Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser. rna splicing, mutation, disease, gene, genomic sequence, nucleotide substitution, deletion, insertion, mutation location, splicing mutation, nucleotide, disease association, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Peking University; Beijing; China
National Natural Science Foundation of China 81001481 PMID:22139928 The community can contribute to this resource biotools:splicedisease_db, nlx_151614 https://bio.tools/splicedisease_db SCR_006130 Splice Disease, SpliceDisease Database Site, Splice Disease Database, SpliceDisease Database 2026-02-11 10:57:15 2
funRiceGenes
 
Resource Report
Resource Website
10+ mentions
funRiceGenes (RRID:SCR_015778) data set, data or information resource, database 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 2026-02-11 10:59:24 44
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) software application, data visualization software, software resource, web service, data analysis software, data access protocol, data processing software 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 2026-02-11 10:59:27 3
REST: a toolkit for resting-state fMRI
 
Resource Report
Resource Website
500+ mentions
REST: a toolkit for resting-state fMRI (RRID:SCR_009641) REST software application, image analysis software, software resource, software toolkit, data processing software, image processing software A user-friendly convenient toolkit to calculate Functional Connectivity (FC), Regional Homogeneity (ReHo), Amplitude of Low-Frequency Fluctuation (ALFF), Fractional ALFF (fALFF), Gragner causality and perform statistical analysis. You also can use REST to view your data, perform Monte Carlo simulation similar to AlphaSim in AFNI, calculate your images, regress out covariates, extract Region of Interest (ROI) time courses, reslice images, and sort DICOM files. correlation, cross-correlation, fourier time-domain analysis, gnome, kde, linux, macos, matlab, microsoft, modeling, magnetic resonance, nifti, posix/unix-like, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, two dimensional display, visualization, windows, resting-state functional magnetic resonance imaging, resting-state fmri is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Beijing Normal University; Beijing; China
National High Technology Program of China ;
National Natural Science Foundation of China ;
Program for Changjiang Scholars and Innovative Research Team in University
PMID:21949842 Academic Free License nlx_155936 http://www.nitrc.org/projects/rest SCR_009641 Resting-State fMRI Data Analysis Toolkit, REsting State fMRI Data analysis Toolkit 2026-02-11 10:57:59 866
clusterProfiler
 
Resource Report
Resource Website
10000+ mentions
clusterProfiler (RRID:SCR_016884) software application, data visualization software, software resource, data analysis software, data processing software Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters. data, statistical, analysis, visualization, gene, cluster, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
is related to: R Project for Statistical Computing
National 973 Projects of China ;
2007 Chang-Jiang Scholars Program ;
National Natural Science Foundation of China ;
Guangdong Natural Science Research Grant ;
Fundamental Research Funds for the Central Universities
PMID:22455463 Free, Available for download, Freely available biotools:clusterprofiler https://github.com/GuangchuangYu/clusterProfiler
https://guangchuangyu.github.io/software/clusterProfiler/
https://bio.tools/clusterprofiler
SCR_016884 Cluster Profiler 2026-02-11 10:59:31 10762
BinPacker
 
Resource Report
Resource Website
10+ mentions
BinPacker (RRID:SCR_017038) software resource, software application, data processing software, data analysis software Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux. de novo, transcriptome, assembler, RNAseq, data, full, length, transcript, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
National Natural Science Foundation of China ;
NSF 1553680;
NCRR P20 RR01 6460;
NIGMS P20 GM103429
PMID:26894997 Free, Available for download, Freely available OMICS_11199, biotools:binpacker http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download
http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download
https://bio.tools/binpacker
SCR_017038 2026-02-11 10:59:37 10
Gene Expression Profiling Interactive Analysis
 
Resource Report
Resource Website
5000+ mentions
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) GEPIA production service resource, software resource, web service, data access protocol, service resource, analysis 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 2026-02-11 10:59:44 5635
GPS-SUMO
 
Resource Report
Resource Website
1+ mentions
GPS-SUMO (RRID:SCR_018261) portal, data or information resource, software resource, web service, data access protocol, service resource 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 2026-02-11 10:59:46 2
PANDA
 
Resource Report
Resource Website
100+ mentions
PANDA (RRID:SCR_002511) PANDA software resource, software toolkit 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 2026-02-11 10:56:29 376
IndelFR - Indel Flanking Region Database
 
Resource Report
Resource Website
1+ mentions
IndelFR - Indel Flanking Region Database (RRID:SCR_006050) IndelFR data or information resource, database THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions. indel, flanking region, protein, structural domain, domain, protein superfamily, protein structure, insertion/deletion, insertion, deletion, protein sequence, sequence, structure, protein domain, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: SCOP: Structural Classification of Proteins
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
has parent organization: Shandong University; Shandong; China
Independent Innovation Foundation of Shandong University 2009JC006;
National Natural Science Foundation of China 30970092;
National Natural Science Foundation of China 61070017;
Scientific Research Reward Fund for excellent Young and Middle-Aged scientists in Shandong Province 20090451326
PMID:22127860 THIS RESOURCE IS NO LONGER IN SERVICE biotools:indelfr, nlx_151448 https://bio.tools/indelfr SCR_006050 IndelFR: Indel Flanking Region Database, Indel Flanking Region Database 2026-02-11 10:57:18 2
Dr.VIS - Human Disease-Related Viral Integration Sites
 
Resource Report
Resource Website
1+ mentions
Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) Dr.VIS, Dr. VIS data or information resource, database Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free. disease, virus, viral integration, viral integration site, integration site, malignant disease, chromosome region, genomic position, viral-host junction sequence, junction sequence, oncogene, chromosome, catalog, graphic interface, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Tongji University; Shanghai; China
State Key Basic Research Program 973 2011CB910204;
National Natural Science Foundation of China ;
Major State Basic Research Development Program ;
863 Hi-Tech Program of China ;
National Key Technology R&D Program in the 11th Five Year Plan of China ;
Major State Basic Research Development Program of China
PMID:22135288 Open - Free to browse and download data in Dr.VIS. nlx_151323, biotools:dr.vis http://www.scbit.org/dbmi/drvis
https://bio.tools/dr.vis
SCR_005965 Dr. VIS - Database of Human Disease-related Viral Integration Sites, Database of Human Disease-related Viral Integration Sites 2026-02-11 10:57:12 1
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit
 
Resource Report
Resource Website
10+ mentions
GOEAST - Gene Ontology Enrichment Analysis Software Toolkit (RRID:SCR_006580) GOEAST data analysis service, service resource, production service resource, analysis service resource 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) 2026-02-11 10:57:22 38
trRosetta
 
Resource Report
Resource Website
50+ mentions
trRosetta (RRID:SCR_021181) simulation software, software resource, software application, 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 2026-02-11 11:00:11 67
CIRIquant
 
Resource Report
Resource Website
1+ mentions
CIRIquant (RRID:SCR_021661) software application, software resource, software toolkit, 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 2026-02-11 11:00:10 1
CIRCexplorer2
 
Resource Report
Resource Website
10+ mentions
CIRCexplorer2 (RRID:SCR_021664) software resource, software application, data processing software, data analysis 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 2026-02-11 11:00:09 40
CancerMIRNome
 
Resource Report
Resource Website
10+ mentions
CancerMIRNome (RRID:SCR_022092) data or information resource, database, software resource, web service, data access protocol 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 2026-02-11 11:00:17 24

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