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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CIRCexplorer2 Resource Report Resource Website 10+ mentions |
CIRCexplorer2 (RRID:SCR_021664) | data analysis software, data processing software, software application, software resource | 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 | Ministry of Science and Technology of China ; National Natural Science Foundation of China |
PMID:27365365 PMID:30539552 |
Free, Available for download, Freely available | SCR_021664 | 2026-08-29 11:27:23 | 49 | |||||||||
|
CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | data access protocol, data or information resource, database, software resource, web service | 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 |
National Natural Science Foundation of China ; Riverside Faculty Start-up Fund ; Science and Technology Project of Guizhou Province ; UC Academic Senate CoR Research Grant ; UC Cancer Research Coordinating Committee Competition Award ; United States Department of Agriculture |
DOI:10.1093/nar/gkab784 | Free, Freely available | SCR_022092 | 2026-08-29 11:27:21 | 48 | ||||||||
|
IOBR Resource Report Resource Website 10+ mentions |
IOBR (RRID:SCR_025619) | data analysis software, data processing software, software application, software resource | Software R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. Used for comprehensively interpreting multi-omics data. | interpreting multi-omics data, perform comprehensive analysis, | Guangzhou Planned Project of Science and Technology ; National Natural Science Foundation of China |
PMID:34276676 | Free, Available for download, Freely available, | SCR_025619 | Immuno-Oncology Biological Research | 2026-08-29 11:34:08 | 44 | ||||||||
|
hTFtarget Resource Report Resource Website 50+ mentions |
hTFtarget (RRID:SCR_025626) | data or information resource, database, software resource, source code | Comprehensive database for regulations of Human Transcription Factors and their targets. Provides tools for visualization, interpretation, and analysis of pathway knowledge. | Human transcription factor database, human transcription factor, pathway knowledge, | China Postdoctoral Science Foundation ; National Key R&D Program of China ; National Natural Science Foundation of China |
PMID:32858223 | Free, Freely available | http://bioinfo.life.hust.edu.cn/hTFtarget | SCR_025626 | 2026-08-29 11:34:16 | 93 | ||||||||
|
stMMR Resource Report Resource Website 1+ mentions |
stMMR (RRID:SCR_025601) | software application, software resource, source code | Software tool for spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation. | spatial domain identification, spatially resolved transcriptomics, multi-modal feature representation, | National Natural Science Foundation of China ; Natural Science Foundation of Shandong Province |
DOI:10.1101/2024.02.22.581503 | Free, Available for download, Freely available, | SCR_025601 | 2026-08-29 11:34:07 | 1 | |||||||||
|
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, | Genomics Data Center Construction of Chinese Academy of Sciences ; International Partnership Program of the Chinese Academy of Sciences ; National Key R and D Program of China ; National Natural Science Foundation of China ; Strategic Priority Research Program of Chinese Academy of Sciences |
PMID:34400360 | r3d100012342 | https://doi.org/10.17616/R3094D | SCR_025826 | Genome Sequence Archive Family, , Genome Sequence Archive | 2026-08-29 11:34:13 | 1805 | ||||||
|
CancerSEA Resource Report Resource Website 100+ 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 | 2026-08-29 11:34:20 | 202 | ||||||||
|
Gene Expression Profiling Interactive Analysis 2 Resource Report Resource Website 1000+ mentions |
Gene Expression Profiling Interactive Analysis 2 (RRID:SCR_026154) | data access protocol, software resource, web service | Enhanced web server for large-scale expression profiling and interactive analysis. GEPIA2 is updated and enhanced version of GEPIA, offering more functionalities, higher resolution data analysis, and additional features like ability to analyze specific cancer subtypes, quantify gene signatures based on single-cell sequencing studies, and allow users to upload their own RNA-seq data for comparison with the TCGA and GTEx datasets; essentially providing more comprehensive and advanced platform for gene expression analysis compared to the original GEPIA version. | gene expression analysis, large-scale expression profiling, interactive analysis, quantify gene signatures, | is related to: Gene Expression Profiling Interactive Analysis | National Natural Science Foundation of China ; Peking University |
PMID:31114875 | Free, Freely available | GEPIA2 | http://gepia2.cancer-pku.cn/ | SCR_026154 | Gene Expression Profiling Interactive Analysis 2 | 2026-08-29 11:34:38 | 1694 | |||||
|
HapHiC Resource Report Resource Website 10+ mentions |
HapHiC (RRID:SCR_026284) | software application, software resource, source code | Software fast, reference-independent, allele-aware scaffolding tool based on Hi-C data. Allele-aware scaffolding tool that uses Hi-C data to scaffold haplotype-phased genome assemblies into chromosome-scale pseudomolecules. | reference-independent, allele-aware scaffolding tool, performance on chromosome assignment, contig ordering and orientation, Hi-C data, scaffold haplotype-phased genome assemblies, chromosome-scale pseudomolecules, | National Natural Science Foundation of China | PMID:39103456 | Free, Available for download, Freely available | SCR_026284 | 2026-08-29 11:34:41 | 27 | |||||||||
|
Coding-Non-Coding Index Resource Report Resource Website |
Coding-Non-Coding Index (RRID:SCR_026554) | CNCI | software application, software resource, source code | Software tool for utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. | utilizing sequence intrinsic composition, classify protein-coding and long non-coding transcripts, | National Natural Science Foundation of China | PMID:23892401 | Free, Available for download, Freely available | SCR_026554 | Coding-Non-Coding Index (CNCI) | 2026-08-29 11:34:50 | 0 | |||||||
|
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 | 2026-08-29 11:34:50 | 0 | |||||||
|
SemiBin Resource Report Resource Website 10+ mentions |
SemiBin (RRID:SCR_026896) | software application, software resource, source code | Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning. | command tool, metagenomic binning, contig level, short and long reads, | National Natural Science Foundation of China ; Shanghai Municipal Science and Technology Major Project |
PMID:35484115 PMID:37387171 |
Free, Available for download, Freely available | SCR_026896 | SemiBin2 | 2026-08-29 11:34:57 | 20 | ||||||||
|
ggVennDiagram Resource Report Resource Website 10+ mentions |
ggVennDiagram (RRID:SCR_026950) | software resource, software toolkit, source code | Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram. | generate Venn diagram, | uses: ggplot2 | Fundamental Research Funds for the Central Universities ; National Key Research Program of China ; National Natural Science Foundation of China ; Royal Society-Newton Advanced Fellowship ; Wuhan Applied Foundational Frontier Project |
PMID:34557218 | Free, Available for download, Freely available | https://github.com/gaospecial/ggVennDiagram | SCR_026950 | 2026-08-29 11:34:58 | 46 | |||||||
|
GFFx Resource Report Resource Website 1+ mentions |
GFFx (RRID:SCR_027445) | software resource, software toolkit, source code | Software Rust-Based suite of utilities for ultra-fast genomic feature extraction. Used for ultra-fast and scalable genome annotation access. Can be used both as a command-line tool and as a Rust library. | genomic feature extraction, genome annotation access, | National Natural Science Foundation of China | DOI:10.1101/2025.08.08.669426 | Free, Available for download, Freely available | https://crates.io/crates/gffx | SCR_027445 | 2026-08-29 11:35:22 | 1 | ||||||||
|
SeedGerm-VIG Resource Report Resource Website 1+ mentions |
SeedGerm-VIG (RRID:SCR_027483) | data analysis software, data processing software, software application, software resource, source code, time-series analysis software | Software pipeline to quantify seed vigour in wheat and other cereal crops using deep learning powered dynamic phenotypic analysis. | seed vigour, germination, vision-based deep learning, dynamic trait analysis, wheat | Allan & Gill Gray Foundation’ Sustainable Productivity for Crop Improvement G118688; BBSRC’s ALERT grant BB/X019683/1; BBSRC’s International Partnership Grant BB/Y514081/1; National Natural Science Foundation of China 32070400 & U24A20402; the United Kingdom Research and Innovation's (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) AI in Bioscience Grant BB/Y513969/1 |
DOI:10.1093/gigascience/giaf129 | Free, Available for download, Freely available | SCR_027483 | 2026-08-29 11:35:24 | 1 | |||||||||
|
ImmuCellAI Resource Report Resource Website 10+ mentions |
ImmuCellAI (RRID:SCR_027645) | software application, software resource, source code | Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy. | Cell subsets abundance prediction, predicting immunotherapy response, cancer immunotherapy estimate, immune cells, gene expression dataset, | National Natural Science Foundation of China | PMID:32274301 | Free, Available for download, Freely available | https://github.com/lydiaMyr/ImmuCellAI | SCR_027645 | Immune Cell Abundance Identifier | 2026-08-29 11:35:25 | 12 | |||||||
|
PanPep Resource Report Resource Website |
PanPep (RRID:SCR_028580) | software application, software resource, source code | Software framework constructed in three levels for predicting the peptide and TCR binding recognition. Used to recognize TCR–antigen binding, by combining the concepts of meta-learning and the neural Turing machine. | predicting peptide and TCR binding recognition, recognize TCR–antigen binding, | National Key Research and Development Program of China ; National Natural Science Foundation of China ; Shanghai Natural Science Foundation Program |
DOI:10.1038/s42256-023-00619-3 | Free, Available for download, Freely available | SCR_028580 | , Pan-Peptide Meta Learning | 2026-08-29 11:35:33 | 0 | ||||||||
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TCellSI Resource Report Resource Website |
TCellSI (RRID:SCR_028753) | data access protocol, software resource, software toolkit, web service | Software R package and web server for T cell state assessment and its applications in immune environment prediction. | T cell state assessment, immune environment prediction, | National Natural Science Foundation of China | PMID:39429885 | Free, Available for download, Freely available | https://github.com/GuoBioinfoLab/TCellSI | SCR_028753 | T cell state identifier (TCellSI) | 2026-08-29 11:35:48 | 0 | |||||||
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ImmuScope Resource Report Resource Website |
ImmuScope (RRID:SCR_028676) | software application, software resource, source code | Software tool to predict CD4+ T cell epitopes, model MHC-II antigen presentation, and assess immune responses. It helps scientists with vaccine design, cancer neoantigen discovery, and tracking viral mutations. | predict CD4+ T cell epitopes, model MHC-II antigen presentation, assess immune responses, | Monash University ; National Health and Medical Research Council of Australia ; National Natural Science Foundation of China |
DOI:10.1101/2025.02.02.636141 | Free, Available for download, Freely available | SCR_028676 | 2026-08-29 11:35:46 | 0 | |||||||||
|
Arabidopsis Hormone Database Resource Report Resource Website 10+ mentions |
Arabidopsis Hormone Database (RRID:SCR_001792) | AHD, AHD2.0 | controlled vocabulary, data or information resource, data repository, database, ontology, service resource, storage service resource | Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions. | arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis service |
is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 30625003; National Natural Science Foundation of China 30730011; Ministry of Science and Technology of China 2009CB119101; Ministry of Education of China ED20060047 |
PMID:21045062 PMID:19015126 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02559 | SCR_001792 | Arabidopsis Hormone Database 2.0 | 2026-08-29 11:20:51 | 28 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
