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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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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 | 2026-08-02 09:03:36 | 376 | ||||
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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 | 2026-08-02 09:08:49 | 3 | ||||||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | data repository, data or information resource, database, storage service resource, 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 | 2026-08-03 09:32:58 | 34 | ||||
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SpliceDisease Resource Report Resource Website 1+ mentions |
SpliceDisease (RRID:SCR_006130) | SpliceDisease | data repository, data or information resource, database, storage service resource, 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 | 2026-08-03 09:33:01 | 2 | ||||
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REST: a toolkit for resting-state fMRI Resource Report Resource Website 500+ mentions |
REST: a toolkit for resting-state fMRI (RRID:SCR_009641) | REST | image processing software, software toolkit, software application, data processing software, image analysis software, software resource | 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 | 2026-08-03 09:34:09 | 866 | ||||
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Residue Iteration Decomposition Resource Report Resource Website 1+ mentions |
Residue Iteration Decomposition (RRID:SCR_022174) | RIDE | software toolkit, software resource | 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 | 2026-08-02 09:08:23 | 5 | ||||||
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GetOrganelle Resource Report Resource Website 100+ mentions |
GetOrganelle (RRID:SCR_022963) | software toolkit, software resource | 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 | 2026-08-02 09:08:34 | 175 | |||||||||
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SciBet Resource Report Resource Website 1+ mentions |
SciBet (RRID:SCR_024743) | simulation software, software resource, software application | 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 | 2026-08-02 09:09:07 | 4 | |||||||||
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funRiceGenes Resource Report Resource Website 10+ mentions |
funRiceGenes (RRID:SCR_015778) | data or information resource, database, 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 | 2026-08-03 09:36:26 | 44 | ||||||||
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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) | web service, software application, data processing software, data analysis software, data access protocol, software resource, data visualization 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 | 2026-08-03 09:36:17 | 3 | |||||||
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clusterProfiler Resource Report Resource Website 10000+ mentions |
clusterProfiler (RRID:SCR_016884) | software application, data processing software, data analysis software, software resource, data visualization 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 | 2026-08-03 09:36:37 | 10762 | |||||
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OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | web service, data access protocol, software resource | 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 | 2026-08-03 09:38:01 | 255 | |||||||||
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Plant mPLoc Resource Report Resource Website 100+ mentions |
Plant mPLoc (RRID:SCR_023014) | web service, data access protocol, software resource | 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 | 2026-08-03 09:38:07 | 105 | ||||||||
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Database Commons Resource Report Resource Website 10+ mentions |
Database Commons (RRID:SCR_023661) | catalog, data or information resource, database | 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 | 2026-08-03 09:38:06 | 13 | |||||||||
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CIRIquant Resource Report Resource Website 1+ mentions |
CIRIquant (RRID:SCR_021661) | software toolkit, software application, data processing software, data analysis software, software resource | 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 | 2026-08-03 09:37:44 | 1 | ||||||||
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CIRCexplorer2 Resource Report Resource Website 10+ mentions |
CIRCexplorer2 (RRID:SCR_021664) | software resource, data processing software, software application, 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 | 2026-08-03 09:37:44 | 40 | |||||||||
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CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | web service, database, data access protocol, data or information resource, 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 | 2026-08-03 09:37:46 | 24 | ||||||||
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Gene Expression Profiling Interactive Analysis Resource Report Resource Website 5000+ mentions |
Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) | GEPIA | production service resource, web service, analysis service resource, data access protocol, service resource, 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 | 2026-08-03 09:37:00 | 5635 | ||||||
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GPS-SUMO Resource Report Resource Website 1+ mentions |
GPS-SUMO (RRID:SCR_018261) | portal, web service, service resource, data access protocol, data or information resource, software 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 | 2026-08-03 09:37:14 | 2 | |||||
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TIMER Resource Report Resource Website 1000+ mentions |
TIMER (RRID:SCR_018737) | TIMER | production service resource, web service, analysis service resource, data access protocol, service resource, software 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 | 2026-08-03 09:37:05 | 2042 |
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