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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Plant mPLoc Resource Report Resource Website 100+ mentions |
Plant mPLoc (RRID:SCR_023014) | data access protocol, software resource, web service | 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 | 2026-02-13 10:58:51 | 105 | ||||||||
|
Human Protein-Protein Interaction Mining Tool Resource Report Resource Website 1+ mentions |
Human Protein-Protein Interaction Mining Tool (RRID:SCR_008040) | software resource, text-mining software, software application | 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 | 2026-02-13 10:56:06 | 1 | ||||||||
|
IOBR Resource Report Resource Website 10+ mentions |
IOBR (RRID:SCR_025619) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-13 10:59:30 | 29 | ||||||||
|
hTFtarget Resource Report Resource Website 10+ mentions |
hTFtarget (RRID:SCR_025626) | data or information resource, software resource, source code, database | 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 | 2026-02-13 10:59:29 | 40 | ||||||||
|
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 | 2026-02-13 10:59:38 | 1 | |||||||||
|
SciBet Resource Report Resource Website 1+ mentions |
SciBet (RRID:SCR_024743) | software resource, simulation software, 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 | 2026-02-13 10:59:21 | 4 | |||||||||
|
Gene Expression Profiling Interactive Analysis 2 Resource Report Resource Website 500+ 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 | 2026-02-13 10:59:32 | 545 | |||||
|
HapHiC Resource Report Resource Website 10+ mentions |
HapHiC (RRID:SCR_026284) | software resource, source code, software application | 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 | 2026-02-13 10:59:38 | 13 | |||||||||
|
Coding-Non-Coding Index Resource Report Resource Website |
Coding-Non-Coding Index (RRID:SCR_026554) | CNCI | software resource, source code, software application | 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) | 2026-02-13 10:59:36 | 0 | |||||||
|
GetOrganelle Resource Report Resource Website 100+ mentions |
GetOrganelle (RRID:SCR_022963) | software resource, software toolkit | 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 | 2026-02-13 10:58:50 | 175 | |||||||||
|
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 | 2026-02-13 10:59:39 | 0 | |||||||
|
ggVennDiagram Resource Report Resource Website 10+ mentions |
ggVennDiagram (RRID:SCR_026950) | software resource, source code, software toolkit | 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 | 2026-02-13 10:59:49 | 37 | |||||||
|
SemiBin Resource Report Resource Website 10+ mentions |
SemiBin (RRID:SCR_026896) | software resource, source code, software application | 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 | 2026-02-13 10:59:40 | 10 | ||||||||
|
GFFx Resource Report Resource Website 1+ mentions |
GFFx (RRID:SCR_027445) | software resource, source code, software toolkit | 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 | 2026-02-13 10:59:56 | 1 | ||||||||
|
SeedGerm-VIG Resource Report Resource Website 1+ mentions |
SeedGerm-VIG (RRID:SCR_027483) | data processing software, data analysis software, source code, time-series analysis software, software application, 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 | 2026-02-13 10:59:57 | 1 | |||||||||
|
ImmuCellAI Resource Report Resource Website 1+ mentions |
ImmuCellAI (RRID:SCR_027645) | software resource, source code, software application | 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 | 2026-02-13 10:59:59 | 6 | |||||||
|
SOAPBarcode Resource Report Resource Website 100+ mentions |
SOAPBarcode (RRID:SCR_015776) | sequencing analysis software | Software for metabarcoding of DNA. SOAPBarcode takes advantage of high throughput capacity of next-generation-sequencing (NGS) platforms and can characterize the biodiversity of large volumes of eukaryote samples. | metabarcoding, metabarcode, bgi, soap, ngs, next generation sequencing, eukaryote | National High-tech Research and Development Project (863) of China 2012AA021601; Yunnan Province 20080A001; Chinese Academy of Sciences 0902281081; Chinese Academy of Sciences KSCX2-YW-Z-1027; National Natural Science Foundation of China 31170498; Ministry of Science and Technology of China 2012FY110800; University of East Anglia |
Free, Available for download | SCR_015776 | metabarcoding | 2026-02-07 02:09:40 | 170 | |||||||||
|
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 | 2026-02-07 02:07:43 | 1 | ||||||||
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Human Potential Tumor Associated Antigen database Resource Report Resource Website 1+ mentions |
Human Potential Tumor Associated Antigen database (RRID:SCR_002938) | data or information resource, database | To accelerate the process of tumor antigen discovery, we generated a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with pTAAs identified by insilico computing. 3518 potential targets have been included in the database, which is freely available to academic users. It successfully screened out 41 of 82 known Cancer-Testis antigens, 6 of 18 differentiation antigen, 2 of 2 oncofetal antigen, and 7 of 12 FDA approved cancer markers that have Gene ID, therefore will provide a good platform for identification of cancer target genes. This database utilizes expression data from various expression platforms, including carefully chosen publicly available microarray expression data, GEO SAGE data, Unigene expression data. In addition, other relevant databases required for TAA discovery such as CGAP, CCDS, gene ontology database etc, were also incorporated. In order to integrate different expression platforms together, various strategies and algorithms have been developed. Known tumor antigens are gathered from literature and serve as training sets. A total tumor specificity penalty was computed from positive clue penalty for differential expression in human cancers, the corresponding differential ratio, and normal tissue restriction penalty for each gene. We hope this database will help with the process of cancer immunome identification, thus help with improving the diagnosis and treatment of human carcinomas. | cancer, tumor, tumor-associated antigen | has parent organization: Chinese Academy of Sciences; Beijing; China | National 863 program in China 2001AA215411; National Natural Science Foundation of China 30531160045; National Natural Science Foundation of China 30570393; Ludwig Institute for Cancer Research KSP 003 |
PMID:16381942 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02987 | http://www.hptaa.org | SCR_002938 | HPtaa Database | 2026-02-11 10:56:40 | 1 | |||||
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Consortium for Reliability and Reproducibility Resource Report Resource Website 1+ mentions |
Consortium for Reliability and Reproducibility (RRID:SCR_003774) | CoRR | data or information resource, portal, data set | Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans | consortium, connectomics, reproducibility, resting state fmri, fmri, diffusion mri, neuroimaging, metadata standard, functional image, dti, anatomical image, functional, anatomical |
uses: Mind Research Network - COINS uses: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project |
NIDA ; National Natural Science Foundation of China ; Child Mind Institute ; Institute of Psychology ; Chinese Academy of Sciences ; Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Registration required, (NITRC), Open unspecified license | nlx_158048 | SCR_003774 | Consortium for Reliability and Reproducibility (CoRR) | 2026-02-12 09:43:40 | 6 |
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