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https://appyters.maayanlab.cloud/#/hTFtarget_Harmonizome_ETL
Comprehensive database for regulations of Human Transcription Factors and their targets. Provides tools for visualization, interpretation, and analysis of pathway knowledge.
Proper citation: hTFtarget (RRID:SCR_025626) Copy
https://github.com/nayu0419/stMMR
Software tool for spatial domain identification from spatially resolved transcriptomics with multi-modal feature representation.
Proper citation: stMMR (RRID:SCR_025601) Copy
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.
Proper citation: Chinese Genome Sequence Archive (RRID:SCR_025826) Copy
https://github.com/PaulingLiu/scibet
Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells.
Proper citation: SciBet (RRID:SCR_024743) Copy
Manually curated database of relations between phase separation and diseases.
Proper citation: PhaSeDis (RRID:SCR_024963) Copy
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.
Proper citation: PhaSepDB (RRID:SCR_024964) Copy
Comprehensive database of RNAs involved in liquid-liquid phase separation.
Proper citation: RPS (RRID:SCR_024960) Copy
https://pmc.ncbi.nlm.nih.gov/articles/PMC3783192/
Software tool for utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Proper citation: Coding-Non-Coding Index (RRID:SCR_026554) Copy
https://github.com/lvrgb777/STPoseNet
Source code for pose recognition model for laboratory mice based on yolov8. Real-time spatiotemporal network model for robust mouse pose estimation.
Proper citation: STPoseNet (RRID:SCR_026834) Copy
https://github.com/BigDataBiology/SemiBin/
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.
Proper citation: SemiBin (RRID:SCR_026896) Copy
https://cran.r-project.org/web/packages/ggVennDiagram/readme/README.html
Software R package to generate Venn diagram.'ggplot2' implement of Venn Diagram.
Proper citation: ggVennDiagram (RRID:SCR_026950) Copy
http://biocc.hrbmu.edu.cn/CancerSEA/
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.
Proper citation: CancerSEA (RRID:SCR_026155) Copy
http://gepia2.cancer-pku.cn/#index
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.
Proper citation: Gene Expression Profiling Interactive Analysis 2 (RRID:SCR_026154) Copy
https://github.com/zengxiaofei/HapHiC
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.
Proper citation: HapHiC (RRID:SCR_026284) Copy
https://github.com/Baohua-Chen/GFFx
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.
Proper citation: GFFx (RRID:SCR_027445) Copy
https://github.com/The-Zhou-Lab/SeedGerm-VIG
Software pipeline to quantify seed vigour in wheat and other cereal crops using deep learning powered dynamic phenotypic analysis.
Proper citation: SeedGerm-VIG (RRID:SCR_027483) Copy
https://guolab.wchscu.cn/ImmuCellAI/#!/
Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy.
Proper citation: ImmuCellAI (RRID:SCR_027645) Copy
https://github.com/bm2-lab/PanPep
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.
Proper citation: PanPep (RRID:SCR_028580) Copy
https://guolab.wchscu.cn/TCellSI/
Software R package and web server for T cell state assessment and its applications in immune environment prediction.
Proper citation: TCellSI (RRID:SCR_028753) Copy
https://github.com/shenlongchen/immuscope
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.
Proper citation: ImmuScope (RRID:SCR_028676) Copy
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