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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||||
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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 | |||||||
|
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 | ||||||||
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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 | |||||||||
|
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 | |||||||
|
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 | |||||||||
|
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 | |||||||
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SciBet Resource Report Resource Website 1+ mentions |
SciBet (RRID:SCR_024743) | simulation software, software application, software resource | 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 | 2026-08-29 11:33:31 | 4 | |||||||||
|
PhaSeDis Resource Report Resource Website 1+ mentions |
PhaSeDis (RRID:SCR_024963) | data or information resource, database | 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 | 2026-08-29 11:33:51 | 4 | ||||||||
|
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 | 2026-08-29 11:33:49 | 36 | |||||||||
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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, | Guangdong Basic and Applied Basic Research Foundation ; National Natural Science Foundation of China ; Program for Guangdong Introducing Innovative and Entrepreneurial Teams |
PMID:34718734 | Free, Freely available | SCR_024960 | 2026-08-29 11:33:38 | 0 | |||||||||
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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 | ||||||||
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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 | |||||||
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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 | ||||||||
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Beijing: Short TR Study Resource Report Resource Website 1+ mentions |
Beijing: Short TR Study (RRID:SCR_003502) | Beijing Short TR | data or information resource, data set | Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information | nifti, fmri, resting-state fmri, image collection, early adult human, mprage, diffusion tensor imaging, neuroimaging, brain, demographic |
has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_157642 | SCR_003502 | Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample, BNU Short TR Sample | 2026-08-29 11:31:52 | 6 | |||||
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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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