# Cosmos-Hub

> A comprehensive documentation on the Cosmos-Hub, the leading cloud-based microbiome analysis software.

## Docs

- [16S Amplicon Classification](https://docs.cosmosid.com/docs/16s-metagenomics-taxonomy.md)
- [PCA](https://docs.cosmosid.com/docs/3d-pca.md): Principal Component Analysis (PCA) is used to visually explore complex data in a way that makes it easier to emphasize variation to bring out strong patterns.
- [About](https://docs.cosmosid.com/docs/about.md)
- [Abundance Distribution](https://docs.cosmosid.com/docs/abundance-distribution.md): Abundance Distribution module allows you to visualize the distribution of individual taxa/features using boxplot across your chosen cohorts.
- [Alpha Diversity](https://docs.cosmosid.com/docs/alpha-diversity.md): Alpha diversity is a fundamental concept in microbiome analysis, measuring the variety of species within a single sample.
- [AMR/VF Profiling](https://docs.cosmosid.com/docs/amr-vf-pipeline.md): The Antimicrobial Resistance (AMR) and Virulence Factor (VF) profiling pipeline in Cosmos-Hub leverages Kepler to provide high-resolution, accurate detection and quantification of resistance and virulence genes from sequencing data. This pipeline uses a sophisticated k-mer-based algorithm and the Re…
- [API Documentation](https://docs.cosmosid.com/docs/api-reference/api-documentation.md): The bioinformatic pipelines within the Cosmos-Hub can be accessed via the Command Line through API integration.
- [Example: Running CHAMP](https://docs.cosmosid.com/docs/api-reference/example-running-champ.md)
- [Install and Setup](https://docs.cosmosid.com/docs/api-reference/install-and-setup.md): These details are written for Terminal on Mac. Please adjust for Windows use.
- [Running the CLI](https://docs.cosmosid.com/docs/api-reference/running-the-cli.md)
- [Example: Running 16S Short-Read](https://docs.cosmosid.com/docs/api-reference/upload_16s.md)
- [Beta Diversity](https://docs.cosmosid.com/docs/beta-diversity.md): Beta diversity is a fundamental concept in microbiome analysis that measures the differences in species composition between multiple samples or cohorts, providing insight into the variation across different environments or conditions.
- [Alpha Diversity Metrics: How to Choose the Right One](https://docs.cosmosid.com/docs/blog/alpha-diversity-what.md)
- [Beta Diversity Metrics: How to Choose the Right One](https://docs.cosmosid.com/docs/blog/beta-diversity-what.md)
- [Extending MaAsLin3: Exporting Input Data and Building Prevalence Models](https://docs.cosmosid.com/docs/blog/extending-ma-as-lin3-how-to-export-input-data-and-build-prevalence-presence-absence-models-in-cosmos-hub.md): Learn how to export MaAsLin3 input data from Cosmos‑Hub and build custom presence/absence logistic regression models aligned with the MaAsLin3 prevalence framework.
- [Bubble Graph](https://docs.cosmosid.com/docs/bubble-graph.md)
- [CHAMP Human Microbiome and Functional Profiling](https://docs.cosmosid.com/docs/champ2.md): This documentation is intended for researchers who require detailed understanding of the CHAMP pipeline architecture, underlying methods, and functional profiling outputs.
- [Collapsible Tree](https://docs.cosmosid.com/docs/collapsible-tree.md)
- [Organize Your Data](https://docs.cosmosid.com/docs/create-folders-and-organize-files.md): View, rename, create folders and move your samples using the sample dashboard
- [Sharing Data](https://docs.cosmosid.com/docs/data-sharing.md): You can easily share profiling data, folders, or comparative analyses with those inside your team network.
- [Database Species Lists](https://docs.cosmosid.com/docs/database-information.md): Use the following links to download species lists for each database.
- [Donut Graph](https://docs.cosmosid.com/docs/donut-graph.md)
- [Raw Data Download](https://docs.cosmosid.com/docs/download-your-raw-fastqs.md): The Cosmos-Hub allows you to store and download your raw fastqs/sequencing data from the dashboard.
- [Exporting Your Profiling Results](https://docs.cosmosid.com/docs/download-your-results.md): You can download your sample results files as well as visualizations and comparative analysis results.
- [Long-Read Amplicon Profiling](https://docs.cosmosid.com/docs/emu.md): Profile long-read amplicon data from Oxford Nanopore or PacBio
- [FASTQC](https://docs.cosmosid.com/docs/fastqc.md)
- [Taxonomic Filtering](https://docs.cosmosid.com/docs/filtering.md): FOR KEPLER RESULTS ONLY: Kepler enables filtering of low-confidence taxa.
- [Functional Host-Agnostic Profiling](https://docs.cosmosid.com/docs/functional-analysis.md): Functional profiling via whole genome shotgun metagenomics or metatranscriptomics provides actionable insights into the molecular, biochemical, and metabolic capacity of microbial communities.
- [Heatmap](https://docs.cosmosid.com/docs/heat-map.md): Cosmos-Hub's heat map visualizes comparative analysis results using a red-to-blue color spectrum, where red indicates high values and blue represents low values.
- [Host Read Removal Workflow](https://docs.cosmosid.com/docs/host-read-removal-workflow.md): In metagenomics, biological specimens are sometimes collected from a tissue of a host that contains a high ratio of host to bacterial DNA. Removal of host DNA can increase precision and accuracy in microbiome profiling, especially for functional data.
- [ITS Amplicon Classification](https://docs.cosmosid.com/docs/its-amplicon.md): Fungal community profiling using ITS amplicon sequencing and the UNITE database
- [Kepler Host-Agnostic Taxonomic Profiling](https://docs.cosmosid.com/docs/kepler-microbiome-profiler.md)
- [LEfSe Biomarker Discovery Analysis](https://docs.cosmosid.com/docs/lefse-biomarker-discovery-analysis.md)
- [MaAsLin2 for Differential Abundance](https://docs.cosmosid.com/docs/maaslin2.md)
- [Running MaAsLin 2 Workflow](https://docs.cosmosid.com/docs/maaslin2-running-workflow.md): We recommend running MaAsLin analyses independent of other comparative analyses. Once the parameters are set, click the Create button to start the MaAsLin2 workflow. Cosmos-Hub will process the data and return the results when the analysis is complete. Depending on the size of the dataset, the analy…
- [Viewing the MaAsLin2 Results](https://docs.cosmosid.com/docs/maaslin2-view-results.md)
- [MaAsLin3 for Differential Abundance](https://docs.cosmosid.com/docs/maaslin3.md): MaAsLin3 (Microbiome Multivariable Association with Linear Models) is the latest iteration of the tool's framework, currently in beta testing.
- [Longitudinal and Complex Association Testing with MaAsLin3](https://docs.cosmosid.com/docs/maaslin3-longitudinal.md)
- [Running MaAsLin3 Workflow](https://docs.cosmosid.com/docs/maaslin3-running-workflow.md)
- [Viewing the MaAsLin3 Results](https://docs.cosmosid.com/docs/maaslin3-view-results.md)
- [Matrix Table](https://docs.cosmosid.com/docs/matrix-table.md)
- [Uploading Metadata](https://docs.cosmosid.com/docs/metadata-and-cohorts.md): Cosmos-Hub streamlines the process of organizing and analyzing your microbiome data by linking it to relevant experimental or sample metadata. Follow these detailed instructions to ensure smooth and efficient metadata integration into your analysis workflows.
- [(Meta)Transcriptomic Analysis in the HUB](https://docs.cosmosid.com/docs/metatranscriptomic-analysis-in-the-hub.md)
- [Compare Samples (Comparative Analysis)](https://docs.cosmosid.com/docs/new-comparative-analysis.md): How to create a new comparative analysis
- [Quickstart](https://docs.cosmosid.com/docs/quick-start.md): An overview of how to get started with Cosmos-Hub and our award winning pipelines.
- [Radial Tree](https://docs.cosmosid.com/docs/radial-tree.md)
- [Read Statistics](https://docs.cosmosid.com/docs/read-statistics.md): The number of reads in each sample compared on a graph.
- [Changing Order and Color of Cohorts in CA Visualizations](https://docs.cosmosid.com/docs/rearranging-cohorts.md): Customize the color and order of cohorts/metadata groups when generating a comparative analysis.
- [RITA Microbiome Assistant](https://docs.cosmosid.com/docs/rita.md): Whether you're navigating a complex dataset, formulating a hypothesis, or preparing a manuscript, RITA is here to help you and your colleagues move faster and smarter.
- [Sample Abundance Table](https://docs.cosmosid.com/docs/sample-dashboard-table.md): The sample abundance table is the main page for viewing individual samples.
- [Uploading Sequencing Data](https://docs.cosmosid.com/docs/sample-upload.md): The Cosmos-Hub supports importing raw FASTQ data for both amplicon and shotgun metagenomic workflows using multiple upload sources.
- [Setting up your account](https://docs.cosmosid.com/docs/setting-up-your-account.md)
- [Stacked Bar Graph](https://docs.cosmosid.com/docs/stacked-bar.md)
- [Stacked Bar Graph](https://docs.cosmosid.com/docs/stacked-bar-graph.md)
- [Sunburst](https://docs.cosmosid.com/docs/sunburst.md)
- [Sample Tags](https://docs.cosmosid.com/docs/tags.md): Tags provide a flexible alternative to metadata fields or folder-based organization .
- [Available Example Datasets](https://docs.cosmosid.com/docs/technical-appendix/available-example-datasets.md): These datasets can be deposited into your account upon request for demo purposes
- [Bacteria And Fungi Database Updates](https://docs.cosmosid.com/docs/technical-appendix/bacteria-and-fungi-database-updates.md): We have updated our Bacteria and Fungi databases.
- [EU GDPR Clause ](https://docs.cosmosid.com/docs/technical-appendix/eu-gdpr.md): Description of your new file.
- [FAQ](https://docs.cosmosid.com/docs/technical-appendix/faq.md)
- [GTDB vs. NCBI Taxonomic Nomenclature](https://docs.cosmosid.com/docs/technical-appendix/gtdb-and-ncbi-taxonomy-comparison.md): The Cosmos-Hub utilizes GTDB-based nomenclature for taxonomic assessment.
- [Methods for Manuscripts](https://docs.cosmosid.com/docs/technical-appendix/methods.md): How to Cite Cosmos-Hub
- [Security and IT Documentation](https://docs.cosmosid.com/docs/technical-appendix/security-it.md): Cosmos-Hub remains committed to maintaining the highest standards in security, compliance, and IT operations.
- [Update Log](https://docs.cosmosid.com/docs/updates.md)
- [Cosmos-Hub Video Tutorials](https://docs.cosmosid.com/docs/video-library.md): Description of your new file.
- [Viewing Single Sample Profiling Data](https://docs.cosmosid.com/docs/view-sample-results.md)
- [Running Data Workflows](https://docs.cosmosid.com/docs/workflows.md): This page describes each of the workflows available in the Cosmos-Hub.
- [Filtering Samples by Metadata](https://docs.cosmosid.com/v2-0/documentation/guides/navigating-the-sample-dashboard/filtering-samples-by-metadata.md)
- [Troubleshooting Common Metadata Upload Errors](https://docs.cosmosid.com/v2-0/documentation/technical-appendix/technical-appendix/metadata-errors.md)

## OpenAPI Specs

- [discovery-openapi](https://docs.cosmosid.com/discovery-openapi.json)
- [example-openapi](https://docs.cosmosid.com/example-openapi.json)
- [v1-openapi](https://docs.cosmosid.com/v1-openapi.json)
- [openapi](https://docs.cosmosid.com/api-reference/openapi.json)

## Optional

- [Multi-Omics with Cmbio](https://cmbio.io/)
- [Contact Support](mailto:help@cosmos-hub.com)
- [Contact Sales](mailto:info@cosmos-hub.com)