ncRNA Database

PlncRNADB

PlncRNADB: Repository of lncRNAs in Plant

CircFunBase

A Database for Functional Circular RNAs

PceRBase

PceRBase: Plant Competing Endogenous RNA DataBase

PlantCircNet

PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks

PncStress

Manually Curated Database of Experimentally Validated Stress-Responsive Non-coding RNAs in Plants

LeafcircBase

The Leaf Circular RNA Resources

AthRiboNC

Arabidopsis thaliana ncRNA coding potential database

ncRNA Hub

A comprehensive compilation of 233 databases/webservers/tools catering to 46 types of ncRNAs.


Plant Database

RiceNetDB

Comprehensive regulatory database on Oryza Sativa based on genome annotation.

CakorDB

A Comprehensive Resource Database for Caragana korshinskii genomics.

SoyOD

An integrated omics database for soybean germplasm and molecular breeding

iP3Dome

iP3Dome: an interactive Plant 3D genome portal

CropGF

A comprehensive physiological traits database covers multiple significant crops

PSGDb

Plant Stress Gene Database (PSGDb) is a comprehensive database resource of providing important annotation information about stress genes existed in plant.


Disease Database

OverCOVID

To tide over COVID-19, the web portal OverCOVID is provided to share bioinformatics resources and information that may contribute to research advances.

Medical information integrated platform

Provide users with a platform to analyze blood routine, liver function, urine routine, bone density.

NDAtlas

Neurodegenerative Disease Atlas (NDAtlas) is a database for the collective information of the proteins involved in NDs, the related PPIs, and interactive visualizations.

LBD

LBD (Lymphoma Biomarker Database) is a manually curated database of literature-supported biomarkers for lymphoma.

HALD

Human aging and longevity database


Single Cell Atlas

Cell Landscape

Cell Landscape is a database of single cell RNA sequencing atlas from multiple species. Click “Browse” on the top of the homepage to get an overview of this website.

hscTE

This is a single cell browser for exploration of gene and transposable element (TE) activities during the endothelial-to-hematopoietic transition (EHT) in human and mouse.

HEMA

This database exhaustively collects hematopoiesis-related single-cell sequencing data to provide an easily accessible resource for in-depth understanding of the complexity of the origin and development of hematopoietic system

MCA | Mouse Cell Atlas

MCA is a public database that uses single-cell RNA sequencing to determine the cell type composition of mouse major organs and build mouse cell Atlas.

HCL - Human Cell Landscape

HCL is a public databases used single-cell RNA sequencing to determine the cell type composition of major human organs and construct a basic scheme for the human cell landscape.

Human Pan-caner Landscape

Using HH-seq to construct a single-cell transcriptome database covering major cancers with high morbidity and mortality in China.

ACA | Axolotl Cell Atlas

ACA is a publlic database used single-cell RNA sequencing to determine the cell type composition of Axolotl and construct a basic scheme for the Axolotl cell Atlas.

Nvwa

Cell Landscapes for Zebrafish, Drosophila, and Earthworm.

CH-ATAC | scATAC Atlas

Using CH-ATAC-seq to profile chromatin accessibility landscapes in vertebrates and invertebrates.

HUATUO

Landscape of cell-type-specific genetic variation of gene regulation.

DCL | Drosophila Cell Landscape

We used single-cell RNA sequencing to determine the cell type composition of Drosophila and construct a basic scheme for the Drosophila cell landscape (DCL).

ZCL | Zebrafish Cell Landscape

Web-based resources for Zebrafish Cell Landscape. We used single-cell RNA sequencing to determine the cell type composition of major zebrafish organs and construct a basic scheme for the Zebrafish Cell Landscape (ZCL).

dscBLAST

A developmental single-cell Basic Local Alignment Search Tool.The dscBLAST is particularly better at developmental data, and it also performs very well on adult data.

ECL | Earthworm Cell Landscape

A Earthworm cell landscape (ECL) websit.We used single-cell RNA sequencing to determine the cell type composition of Earthworm and construct a basic scheme for the Earthworm cell landscape (ECL).


Tools

CircPlant

An integrated tool to detect circRNAs and interactions with miRNAs in plants

CircPro

CircPro: an integrated tool for the identification of circRNAs with protein-coding potential

MiRNA Digger

Tool for large-scale identifiction of the new microRNA genes by screening the cleavage signals resided within the genome.

Plant MicroRNA Tools

sRNA analysis tool

CytoSEE

A web-based toolkit for automatic computation and evaluation of cytometry data.

CES

Based on the clonal evolution theory, we construct a deliberately simplified model to simulate tumor progressionBased on the clonal evolution theory, we construct a deliberately simplified model to simulate tumor progression.

DARSEP

Antigenic variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization

PBSK Browser | for systems biology

PBSK Browser for systems biology is a web service for reading some standard file formats of biological pathway, including PSI-MI, BioPAX, SBML and KGML.

Repeater

A platform for genome-wide repeats analysis

Bach

A gene composer software that optimizes coding sequences and calculates corresponding RiPS to illustrate their translation rates

MTide

MTide: an integrated tool for the identification of miRNA-target interaction in plants

pCompare

An R package for position effect comparison on short oligonucleotide microarrays

LncLSTA

A deep learning frame for predicting subcellular localization information of lncRNA and miRNA

DeepTrio

A ternary prediction system for protein-protein interaction using mask multiple parallel convolutional neural networks

RepLoc

A bioinformatic tool which quantifies the sequence repetitiveness based on weighted k-mer coverage

T4SEpp

A unified T4SE prediction pipeline based on deep learning model

BNArray

An R package for constructing gene regulatory networks from microarray data using Bayesian network

CloneAssistant 2.0

An updated version for cloning primer design with significantly expanded utilities

DaTo

DaTo: The atlas of biological database and Tools


Other Database

TreeIN

A Predicted Trichoderma reesei Interactome Network

BioPepDB

BioPepDB is a searchable database of food-derived bioactive peptides and their related articles, including more than four thousand bioactive peptide entries.

Pepward

A database of anticancer peptides, searchable by peptide name, uniprot ID, cancer type, origin and sequence.

STCDB

An Integrative Database for Cell Signal Transduction Classification Alignment


Education

OnlineJudge

An online programming platform designed for bioinformatics programming enthusiasts and learners.

Bio Guide

Collections of various biology databases and tools

SCIIF

A practical SCI IF Search Engine

101计划

教育部生物科学“101计划”生物信息学核心课程及虚拟教研室建设平台