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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-03 09:38:55 | 20 | |||||||||
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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, | 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 | 2026-08-03 09:38:23 | 0 | |||||||||
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IOBR Resource Report Resource Website 10+ mentions |
IOBR (RRID:SCR_025619) | software resource, data processing software, software application, data analysis software | 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, | National Natural Science Foundation of China ; Guangzhou Planned Project of Science and Technology |
PMID:34276676 | Free, Available for download, Freely available, | SCR_025619 | Immuno-Oncology Biological Research | 2026-08-03 09:38:34 | 29 | ||||||||
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stMMR Resource Report Resource Website 1+ mentions |
stMMR (RRID:SCR_025601) | software resource, source code, software application | 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 | 2026-08-03 09:39:10 | 1 | |||||||||
|
hTFtarget Resource Report Resource Website 10+ mentions |
hTFtarget (RRID:SCR_025626) | data or information resource, software resource, database, 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, | National Natural Science Foundation of China ; National Key R&D Program of China ; China Postdoctoral Science Foundation |
PMID:32858223 | Free, Freely available | http://bioinfo.life.hust.edu.cn/hTFtarget | SCR_025626 | 2026-08-03 09:38:35 | 40 | ||||||||
|
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, | 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 | r3d100012342 | https://doi.org/10.17616/R3094D | SCR_025826 | Genome Sequence Archive Family, , Genome Sequence Archive | 2026-08-03 09:39:12 | 1031 | ||||||
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CancerSEA Resource Report Resource Website 50+ 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 | 2026-08-03 09:38:42 | 80 | ||||||||
|
Gene Expression Profiling Interactive Analysis 2 Resource Report Resource Website 500+ mentions |
Gene Expression Profiling Interactive Analysis 2 (RRID:SCR_026154) | web service, data access protocol, software resource | 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 | 2026-08-03 09:38:53 | 545 | |||||
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HapHiC Resource Report Resource Website 10+ mentions |
HapHiC (RRID:SCR_026284) | software resource, software application, 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 | 2026-08-03 09:38:45 | 13 | |||||||||
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Coding-Non-Coding Index Resource Report Resource Website |
Coding-Non-Coding Index (RRID:SCR_026554) | CNCI | software resource, software application, 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) | 2026-08-03 09:39:18 | 0 | |||||||
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ggVennDiagram Resource Report Resource Website 10+ mentions |
ggVennDiagram (RRID:SCR_026950) | software toolkit, software resource, source code | Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram. | generate Venn diagram, | uses: ggplot2 | National Natural Science Foundation of China ; Royal Society-Newton Advanced Fellowship ; National Key Research Program of China ; Wuhan Applied Foundational Frontier Project ; Fundamental Research Funds for the Central Universities |
PMID:34557218 | Free, Available for download, Freely available | https://github.com/gaospecial/ggVennDiagram | SCR_026950 | 2026-08-03 09:39:00 | 37 | |||||||
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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 | 2026-08-03 09:39:22 | 0 | |||||||
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SemiBin Resource Report Resource Website 10+ mentions |
SemiBin (RRID:SCR_026896) | software resource, software application, 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 | 2026-08-03 09:39:01 | 10 | ||||||||
|
GFFx Resource Report Resource Website 1+ mentions |
GFFx (RRID:SCR_027445) | software toolkit, software resource, 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 | 2026-08-03 09:39:08 | 1 | ||||||||
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SeedGerm-VIG Resource Report Resource Website 1+ mentions |
SeedGerm-VIG (RRID:SCR_027483) | software application, data processing software, source code, data analysis software, time-series analysis software, software resource | 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 | National Natural Science Foundation of China 32070400 & U24A20402; Allan & Gill Gray Foundation’ Sustainable Productivity for Crop Improvement G118688; the United Kingdom Research and Innovation's (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) AI in Bioscience Grant BB/Y513969/1; BBSRC’s International Partnership Grant BB/Y514081/1; BBSRC’s ALERT grant BB/X019683/1 |
DOI:10.1093/gigascience/giaf129 | Free, Available for download, Freely available | SCR_027483 | 2026-08-03 09:39:10 | 1 | |||||||||
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ImmuCellAI Resource Report Resource Website 1+ mentions |
ImmuCellAI (RRID:SCR_027645) | software resource, software application, 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 | 2026-08-03 09:39:11 | 6 | |||||||
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PanPep Resource Report Resource Website |
PanPep (RRID:SCR_028580) | software resource, software application, 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 | 2026-08-03 09:39:25 | 0 | ||||||||
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TCellSI Resource Report Resource Website |
TCellSI (RRID:SCR_028753) | web service, data access protocol, software toolkit, software resource | 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) | 2026-08-03 09:39:46 | 0 | |||||||
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ImmuScope Resource Report Resource Website |
ImmuScope (RRID:SCR_028676) | software resource, software application, 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, | National Natural Science Foundation of China ; National Health and Medical Research Council of Australia ; Monash University |
DOI:10.1101/2025.02.02.636141 | Free, Available for download, Freely available | SCR_028676 | 2026-08-03 09:39:38 | 0 | |||||||||
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MedBlast Resource Report Resource Website 1+ mentions |
MedBlast (RRID:SCR_008202) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs. | gene, article, biological, data, genome, genomic, homolog, literature, medline interfaces, mining, molecular, protein, sequence, specie | National Natural Science Foundation of China 39990600-03; Knowledge Innovation Program of the Chinese Academy of Sciences KSCX2-2-07; Knowledge Innovation Program of the Chinese Academy of Sciences KJCX1-08 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21253 | SCR_008202 | MedBlast | 2026-08-01 12:03:28 | 1 |
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