生物信息与智能医学-平台系统

Database-Pairpot

Pairpot

Pairpot is a database tailored for paired single-cell and SRT data with real-time heuristic analysis. It constructs the curated pairs by integrating multiple slices and establishing potential associations between single-cell and SRT data. On this basis, Pairpot adopts semi-supervised learning that enables real-time heuristic analysis where Lasso-View refines the user-selected SRT domains within milliseconds, Pair-View infers cell proportions of spots based on user-selected cell types in real-time and Layer-View displays SRT slices using a 3D hierarchical layout.

2024-11-06

Tool-De-spot

De-spot

De-spot is a bioinformatics tool that enables precise detection of cell-type-specific domains in both spot-level and single-cell spatial resolved transcriptomics (SRT) slices. De-spot bridges the gap between cell-type proportions and spatial domains by integrating potential candidates, inferring enrichment regions of cell-type proportions, and mapping enrichment regions to spatial domains. Using De-spot, researchers could effectively explore cell-type-specific domains and their co-localization information through the 3D Landscapes.

2024-10-28

DataBase-vertebrate

DupScan

DupScan is a database for visualizing and predicting vertebrate synteny and genome duplication. It provides specialized functions to analyse the computation-consuming WGD events by visualizing macro-synteny/micro-synteny, chromosome structures, gene/gene family evolution pattern, Ka/Ks/4DTV distributions.

2022-08-01

DataBase-NeoTCR

NeoTCR

NeoTCR is an immunoinformatic database of T-cell receptor (TCR) sequences with neoantigen specificities. Its primary goal is to facilitate access to existing information on neoantigen-specific TCRs and provide useful web-based tools for comprehensive analysis of TCR sequencing data. It will serve as a valuable platform to study the role of neoantigen-associated T-cells in anti-tumor immunity and further improve the understanding of biological functions and applications of neoantigen-specific TCRs.

2024-05-03

Tool-Hi-C

LPAD

LPAD is an algorithm used to identify TAD structures from Hi-C contact matrices. It employs a random-restart random walk algorithm to construct an undirected graph. Subsequently, a linear method is employed to partition the global, large-scale network graph into smaller subgraphs. An improved label propagation algorithm is then used to identify community structures within the graph, classifying them as TADs, TAD boundaries, TAD gaps.

2023-05-03

Tool-Browser

HiBrowser

HiBrowser is an interactive and dynamic browser specifically designed for the visualization of synchronized Hi-C data. It offers a range of advanced features, including multi-omics synchronized navigation, multi-mode heatmap overlay, synchronized navigation across multiple samples aligned to different reference genomes, interactive 3D simulation models, and precise searching of long-range cis-regulatory elements.

2022-08-01

DataBase-Neoantigens

NeoPetide

NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunological resources. NeoPeptide could help researchers identify neoantigens in different cancers and search for appropriate cancer vaccine candidates.

2019-12-09

DataBase-CPMCP

CPMCP

CPMCP is a traditional Chinese medicine(TCM)-related database. It demonstrates the prescription information of Chinese patent medicines(CPMs) and ancient Chinese medicine prescriptions(CMPs). The database reports their comprehensive and standardized information such as the components, indications, and contraindications. CPMCP is committed to promoting the modernization of TCM and making greater contributions to modern medicine(MM).

2022-11-02

Tool-MACFC

MACFC

MACFC introduces multi-variable Area Under the receiver operating characteristic Curve (AUC) to globally evaluate the complementarity among features by employing Area Above the receiver operating characteristic Curve (AAC).Furthermore, MACFC proposes an AAC-based feature selection algorithm, named Multi-variable AUC-based Combined Features Complementarity, to screen discriminative complementary feature combinations.

2022-11-02

Tool-Fungus

PFGI

PFGI firstly deals with the approaches of the identification and annotation of fungal genomes based on short and long reads sequenced by using multiple platforms to overcome the lack of sufficient approaches for the identification and functional annotation.

2020-12

Tool-Bacteria

PBGI

PBGI is an automated bioinformatics pipeline for customized bioinformatics analysis using both short-reads and long-reads sequencing data produced by multiple platforms that can improve the situation that applying microbiological genomic information.

2020-01