ArtSpaces is a comprehensive resource platform designed to support brain research through multidimensional data and advanced analytical tools. The module consists of nine submodules: AtlasScope, RegionScope, TissueScope, SpaceScope, PathoScope, AgeScope, cPandora, ePandora, sPandora. The first six submodules present atlas of species, brain regions, tissues, spatial data, disease, and evolution. The last three submodules offer analytical tools: PAN Dimensional Rapid Analyzer for a cell type, PAN Dimensional Rapid Analyzer for an entire gene list, and sPandora, PAN Dimensional Rapid Analyzer for a single gene, enabling users to deeply explore and analyze brain tissues and functions.
What is the purpose of the Bodhi module?
Bodhi is a high-throughput brain omics and deep-learning analysis platform designed to facilitate advanced research across species and data types. The module consists of 12 submodules: MissGene, In2Cell, SpaceTeller, Teddi, EvoPred, RecallST, DrSpace, DrWho, DrDance, DrSdrugle, DrOrg, DrRegion. The first six submodules provide tools for cross-species perturbation prediction, bulk RNA-seq deconvolution, spatial transcriptomics analysis, efficient data downsampling, automatic cell-type prediction, and development gap bridging. The latter six submodules extend the platform's functionality for deeper exploration and novel analysis capabilities. Bodhi enables researchers to leverage multi-species data integration and cutting-edge computational tools for comprehensive insights into brain function, development, and disease.
What is the purpose of the CytoPedia module?
CytoPedia is a comprehensive module designed to support cellular and tissue research with advanced tools and multi-dimensional data analyses. The module comprises 12 submodules: Rats, Tiger, Rabbit, Cattle, Dragon, Horse, Sheep, Snake, Rooster, Dog, Pig, Monkey. These submodules offer specialized resources, such as receptor-target screening, trajectory inference from gene expression, regulator analysis for single-cell omics, and cross-species ortholog research targeting evolutionary studies.
What is the purpose of the Dome module?
Dome is an integrative platform designed to explore gene sets and pathways relevant to key biological processes and diseases. The module consists of 10 submodules: StemAtlas, AgingMap, DizPrint, DeathScape, LifeSig, EasyMeta, BioDrug, ArmRace, GeneSetsPedia, SearchDIY.
What is the purpose of the Echo module?
Echo is an advanced platform for the analysis and visualization of epigenomic ATAC-seq data. The module consists of 10 submodules and more that collectively provide comprehensive tools for multi-species epigenomic data exploration. Echo enables researchers to access and analyze peaks information, perform data annotation, explore gene expression patterns, and leverage various analytical tools for deeper insight into epigenomic regulation across species. This platform supports a streamlined workflow for epigenomic research, enhancing the understanding of regulatory landscapes and chromatin accessibility in diverse biological contexts.
What is the purpose of the Falcon module?
Falcon is a versatile platform dedicated to comparative analysis across various datasets, enabling researchers to explore similarities and differences across different biological contexts. The module comprises submodules such as PathoCompare, AgingCompare, RegionCompare, InvertebratesComp, SexCompare, TissueCompare, OrganoidCompare, WeekCompare, EmbryoCompare, ReptilesCompare, and SearchDIY. These tools allow users to perform in-depth comparisons of pathologies, aging, regions, tissues, and more across multiple species and developmental stages. Falcon empowers researchers with the ability to draw comprehensive insights through systematic cross-comparative studies, enhancing their understanding of complex biological phenomena.
What is the purpose of the Ghost module?
Ghost is a specialized module designed to deliver comprehensive profiles for single genes, facilitating in-depth exploration and analysis. The module provides detailed visualizations and data for gene expression across various biological contexts. Ghost equips researchers with the ability to generate precise and detailed gene-centric insights, supporting advanced genomic and functional studies.
What is the purpose of the Help module?
The Help module provides essential resources and guidance for users of BrainStorm, ensuring smooth navigation and effective usage of all its tools and data sets. The module comprises submodules such as Statistics, Tutorial, Acknowledgement, News, Download, Upload, PIclub, GuidingData, UserFeedback, and YellowPages.
What is the purpose of the In2Brain module?
In2Brain is a comprehensive module dedicated to the exploration and profiling of various brain regions. This module includes FrontalCortex, OccipitalCortex, OlfactoryBulb, TemporalCortex, BasalNuclei, Amygdala, LateralHypothalamus, LateralStriatum, and more brain regions, providing researchers with the ability to analyze gene expression, cellular composition, and other relevant data across these critical brain areas.
What is the purpose of the Jumper module?
Jumper is an analysis and visualization platform dedicated to the study of transposable elements. The module includes submodules SLEEPDOG such as SINES, LINES, ERVS, Endogenous-non-LTR, Pseudogene, YoungTEs, DNA transposons, OldTEs, and Gypsy. Jumper empowers researchers with tools for comprehensive exploration, aiding in the understanding of their roles in genome dynamics, evolution, and potential impacts on gene regulation.
What is the purpose of the KeyReg module?
KeyReg provides comprehensive profiling of key regulatory genes in the nervous system. This module includes submodules such as FOXG1, LHX2, UNCX, EGR1, NEUROD1, TBR1, SOX2, PAX6, OLIG2, REST, and TBR2, (FLUENTSPORT)offering detailed insights into their functions and regulatory roles. KeyReg is a useful tool for researchers aiming to understand the gene networks that shape neural development, functionality, and potential contributions to neurological disorders.
What is the purpose of the Landscape module?
The Landscape offers a comprehensive overview of 28 distinct aspects, each delivering detailed insights into unique facets of neuroscience. From gene portraits (GenPortrait) and cell portraits (OnePortrait) to specialized areas like disease (DizPortrait), spatial (SpacePortrait), and age-specific analyses (AgePortrait), each one delves deeply into a particular dimension. Additionally, advanced tools for research-such as computing tools (NovelComputingTools), databases (DatabasePedia), and technology rankings (TechRank)-provide a robust foundation for data-driven discoveries. Lanscape serves as a panoramic resource for exploring genetic, cellular, technological, and clinical nuances, empowering researchers to investigate neural complexity and diversity comprehensively.
What is the purpose of the MolFinger module?
MolFinger is a module dedicated to providing detailed molecular fingerprints for various diseases. This module includes exploration of diseases listed in the menu, such as dementia, epilepsy, early Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Isolated focal cortical dysplasia, Neuralgia, and Depressive disorder. Additionally, MolFinger supports comprehensive analysis beyond these eight conditions, enabling researchers to explore a broader range of diseases.
What is the purpose of the Network module?
Network is a module designed to showcase interaction networks under diverse conditions. There are 12 submodules including ParkinsonNet, AmygdalaNet, SenegalBichirNet, TurbotNet, AgingNet, ReedfishNet, EmbryoNet, CerebralNet, EelNet, PrionNet, ION_Net, Epilepsy_Net and SearchDIY. This module offers comprehensive visualizations of various interaction types, including cell-to-cell (C2C), gene-to-gene (G2G), virus-host interactions, and protein-protein interactions (PPI). Network empowers researchers to explore the intricate web of biological interactions, aiding in the understanding of connectivity and regulatory mechanisms within different conditions.
What is the purpose of the Organogenesis module?
Organogenesis is dedicated to profiling organ development-related atlases across multiple species. It includes nine submodules: Pan_troglodytes, iPSC_Human, Nothobranchius furzeri, Gallus gallus, Pan paniscus, Oryctolagus cuniculus, Nematostella vectensis, Gorilla gorilla, and SearchDIY. This module provides comprehensive insights into embryonic development, organoid studies, and iPSC-related data, enabling researchers to explore developmental processes at various stages and conduct comparative analyses across different species.
What is the purpose of the Pathology module?
Pathology provides a comprehensive portrait for a diverse range of diseases. This module covers conditions such as Huntington's disease, Epilepsy, Aging, Lewy body dementia, Traumatic brain injury, High-grade gliomas, Chronic traumatic encephalopathy, Amyotrophic lateral sclerosis, Rett syndrome, and Early Alzheimer's disease. It offers detailed insights into the pathology, mechanisms, and potential research avenues for these diseases, empowering researchers to delve deeper into neurological and systemic disease studies
What is the purpose of the QuickCompute module?
QuickCompute is a rapid calculation platform designed for large-scale data analysis. This module comprises submodules such as Predict (cell identity prediction), Expression (gene-level expression atlas), Enrichment (easy enrichment of gene lists), and other essential tools for seamless and comprehensive analysis.
What is the purpose of the RegenMed module?
RegenMed module offers a comprehensive resource for regenerative medicine research. It includes sections on bio-regeneration, aging mouse models, drug interventions, mesenchymal stem cells (MSC), induced pluripotent stem cells (IPSCs), naive embryonic stem cells (ESCs), and organoids, alongside insights into transplantation and Notch knockout studies. Researchers can explore gene and cell-based therapies and apply enrichment analyses within these areas. Additionally, the module features a DIY search option .
What is the purpose of the SpeciesEvo module?
SpeciesEvo module specializes in the analysis of genes involved in gene transfers, rapid evolution, species-specific adaptations, and other key genetic features. It enables researchers to explore correlations between different gene sets, perform enrichment analysis, and investigate gene expression patterns across species, tissues, and developmental stages. The module also includes tools for studying evolutionary conserved genes, repeat genes, and young genes, along with a DIY search option for customized exploration.
What is the purpose of the Trajectory module?
Trajectory module provides a suite of tools for in-depth gene expression analysis. It includes trajectory inference from gene expression data, insights into organogenesis regulators in developmental cells, and GO enrichment analysis using cluster profiler. Users can explore gene-level expression, perform unbiased reviews of cell type and lineage expression across time scales, and analyze hallmark gene expression patterns. Additionally, the module allows for easy gene list enrichment and offers a DIY search feature for personalized analysis.
What is the purpose of the UKSC module?
United Kingdom of Single Cell (UKSC) module encodes approximately 10 million cells, assigning each a unique passport. This passport serves as a visualization and cadastral management system for single cells, featuring a picture of the cell and key details such as species origin, developmental stage, tissue source, cell type, physiological status, and an identifier. With direct visualization of each cell, basic science researchers can perform single-cell analysis more efficiently.
What is the purpose of the Visualization module?
Visualization module offers a comprehensive set of tools designed to enhance genomic analysis and research. It provides advanced capabilities for gene visualization, ontology enrichment, association analysis, and transcriptional pairing. Researchers can utilize this module to perform in-depth genomic investigations, analyze gene relationships, and visualize complex datasets, making Visualization module an essential resource for uncovering functional insights and interactions within genomic data.
What is the purpose of the Wonder4Cell module?
The Wonder4Cell module offers a comprehensive atlas of eight distinct brain cell types, providing an integrated view of the cellular landscape in the brain. Each map within the L8 module focuses on a specific cell type, allowing users to explore their unique properties, gene expression profiles, and functional roles. This module is an essential resource for understanding the diversity of brain cells and their contributions to both normal and pathological brain functions, offering a valuable tool for researchers studying brain development, diseases, and cellular interactions.
What is the purpose of the Xomics module?
Xomics provides introduction for OneOmics, SNPomics, ClinicalOmics, ATACseq, RNAseq, SpatialOmics: OneOmics for cell portrait, SNPomics for genetic variant analysis, ClinicalOmics for clinical applications, ATAC-seq for chromatin accessibility, RNA-seq for transcriptome profiling, and SpatialOmics for spatial gene expression. Together, these modules offer comprehensive tools for exploring and interpreting complex biological data across multiple molecular layers.
What is the purpose of the Young4ever module?
Young4ever provides comprehensive profiling of gene sets related to aging. This module encompasses various submodules, including YoungEnriched, OldEnriched, UnionEnriched, NeuroAging, GenomeInstability, SenMayo, TranscriptionFactor, ERV_AIR, and Receptors, all focusing on aspects of aging and associated genetic changes. Young4ever offers researchers valuable insights into age-associated gene expressions, cellular changes, and molecular mechanisms, facilitating deeper understanding and exploration of the aging process.
What is the purpose of the Zootopia module?
Zootopia illustrates the key modules of a gene expression analysis platform, covering resources for gene expression data like background tables for gene expression,
