Why choose CDIAM for 10x Visium HD and Visium data analysis?
Simple deployment and access
CDIAM is an SAAS framework - meaning no installation. You can access the platform anywhere via common web browsers: Chrome, Firefox, Edge, Safari, you name it. The platform can be deployed either behind your organizations' firewall or using private cloud configurations.
Microservices for customization
The microservice-based architecture of CDIAM enables bespoke development, integration with public or internally built pipelines and tools (like R shiny data visualization applications) or even the ability to bring CDIAM capabilities to existing in-house computational resources.
Graphical user interface for ease of use
CDIAM aims to make it easier for all scientists to interpret and leverage the values of omics data. Thus, it is built in an interactive and intuitive graphical UI that is accessible to all biologists, regardless of their programming skills.
Data management and analysis -All in one place
The platform manages the data as individual datasets or groups them in ‘projects’. Multi-omics data in a ‘project’ can be collectively analyzed for aggregate insights, or individually explored. Examples of such aggregate insights include: top ligand-receptor pairs, top cell types interacting with each other, overlapping significant pathways, potential targets, etc. commonly found across experiments.
Save your time for the insights, not the hassle
Visium and Visium HD data analysis is no easy task! It usually takes a lot of programming skills and time to explore suitable analysis packages. In addition, few scalable platforms can handle huge numbers of data points, especially for Visium HD data.
Start analyzing Visium and Visium HD data instantly and easily with CDIAM's interactive and intuitive graphical UI plus pre-built analytical pipelines and workflows.
Take a deep dive into your Visium and Visium HD spatial data end to end
Get all the essentials for Visium and Visium HD data exploration in one single platform, from pre-processing, QC-ing, integrating to visualizing the data and downstream analysis.
Filter & QC
Explore the distribution of your data through various QC plots and apply filtering parameters
Import multi slides
Import multiple Visium tissue slides to view them side by side, or in an integrated UMAP with batch effects corrected using Harmony
Visualize
Visualize clusters and gene expression with different plot types (e.g. scatter plot, violin plot and heatmap), across different coordinates (e.g. UMAP and spatial coordinates)
Find marker genes, DEGs and pathways
Find DE genes and enriched pathways for a region of interest using Reactome, Wikipathways, NCI PID or custom gene sets
Prioritize targets & validate biomarkers
Find and score potential targets and biomarkers through Pathway2Targets and Biomarker2Validate pipelines
Predict intercellular signaling
Study cell-cell communication and identify differential ligand-receptor pairs between experiment and control groups
Overlay expression on morphology images
Add morphological images and overlay spots or squares on them. View gene expression coupled with morphology.
Study gene colocalization and coexpression
Calculate gene colocalization scores and coexpression scores across the tissue slide
Cluster & subcluster
Adjust clustering resolution and cluster your data using Leiden clustering. Sub-clustering enables more detailed focus on a region of interest on the tissue slide.
Explore public and in-house data, together
CDIAM integrates in itself a curated database of public spatial transcriptomics as well as other omics data, where you can interactively access and copy public datasets to your own projects for integration.
Some of the available databases:
10x Genomics Spatial Visium
Pythia curated scRNA-seq database
CosMx
Recount3
CPTAC
Interactively visualize your Scanpy results
Beside feature-barcode matrices, you can submit Scanpy objects (.H5AD) as an input for Visium and Visium HD spatial transcriptomics data. This enables interactive visualization of your Scanpy results, adapability with in-house analysis pipelines and reinforces collaboration among computational biologists and bench scientists.
Go beyond Visium and Visium HD transcriptomics
CDIAM is designed for multi-omics data analysis and integration. Visium and Visium HD spatial data in a project can be collectively analyzed with other omics datasets and experiments for aggregate insights. Easily summarize and validate DE genes, targets, biomarkers, ligand-receptor pairs and pathways across different studies and experiments.
Analyze any where. Collaborate any time.
Access and analyze your data on the web
CDIAM is a web platform, meaning that you can access it and analyze the data any time, any where.
Share and collaborate easily
Collaborate seamlessly with your team members through convenient sharing and collaboration options, such as URLs and shared project notebooks.
Discover important insights with CDIAM
Request a trial now to start analyzing your multi-omics data with CDIAM Multi-Omics Studio.