# Cosmos-Hub

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

- [about](https://docs.cosmosid.com/docs/about.md)
- [Quickstart](https://docs.cosmosid.com/docs/quick-start.md): An overview of how to get started with Cosmos-Hub and our award winning pipelines.
- [Setting up your account](https://docs.cosmosid.com/docs/setting-up-your-account.md)
- [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.
- [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.
- [Running Data Workflows](https://docs.cosmosid.com/docs/workflows.md): This page describes each of the workflows available in the Cosmos-Hub.
- [Compare Samples (Comparative Analysis)](https://docs.cosmosid.com/docs/new-comparative-analysis.md): How to create a new 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.
- [Cosmos-Hub Video Tutorials](https://docs.cosmosid.com/docs/video-library.md): Description of your new file.
- [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
- [Filtering Samples by Metadata](https://docs.cosmosid.com/v2-0/documentation/guides/navigating-the-sample-dashboard/filtering-samples-by-metadata.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.
- [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.
- [Sample Tags](https://docs.cosmosid.com/docs/tags.md): Tags provide a flexible alternative to metadata fields or folder-based organization .
- [Viewing Single Sample Profiling Data](https://docs.cosmosid.com/docs/view-sample-results.md)
- [Sample Abundance Table](https://docs.cosmosid.com/docs/sample-dashboard-table.md): The sample abundance table is the main page for viewing individual samples.
- [Sunburst](https://docs.cosmosid.com/docs/sunburst.md)
- [Bubble Graph](https://docs.cosmosid.com/docs/bubble-graph.md)
- [Collapsible Tree](https://docs.cosmosid.com/docs/collapsible-tree.md)
- [Radial Tree](https://docs.cosmosid.com/docs/radial-tree.md)
- [Donut Graph](https://docs.cosmosid.com/docs/donut-graph.md)
- [Stacked Bar Graph](https://docs.cosmosid.com/docs/stacked-bar-graph.md)
- [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.
- [(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
- [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.
- [Matrix Table](https://docs.cosmosid.com/docs/matrix-table.md)
- [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.
- [Stacked Bar Graph](https://docs.cosmosid.com/docs/stacked-bar.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.
- [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.
- [Alpha-diversity](https://docs.cosmosid.com/docs/alpha-diversity.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.
- [Read Statistics](https://docs.cosmosid.com/docs/read-statistics.md): The number of reads in each sample compared on a graph.
- [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.
- [Running MaAsLin3 Workflow](https://docs.cosmosid.com/docs/maaslin3-running-workflow.md)
- [Longitudinal and Complex Association Testing with MaAsLin3](https://docs.cosmosid.com/docs/maaslin3-longitudinal.md)
- [Viewing the MaAsLin3 Results](https://docs.cosmosid.com/docs/maaslin3-view-results.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.
- [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.
- [Kepler Host-Agnostic Taxonomic Profiling](https://docs.cosmosid.com/docs/kepler-microbiome-profiler.md)
- [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.
- [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…
- [Long-Read Amplicon Profiling](https://docs.cosmosid.com/docs/emu.md): Profile long-read amplicon data from Oxford Nanopore or PacBio
- [16S Amplicon Classification](https://docs.cosmosid.com/docs/16s-metagenomics-taxonomy.md)
- [ITS Amplicon Classification](https://docs.cosmosid.com/docs/its-amplicon.md): Fungal community profiling using ITS amplicon sequencing and the UNITE database
- [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.
- [Database Species Lists](https://docs.cosmosid.com/docs/database-information.md): Use the following links to download species lists for each database.
- [Methods for Manuscripts](https://docs.cosmosid.com/docs/technical-appendix/methods.md): How to Cite Cosmos-Hub
- [Update Log](https://docs.cosmosid.com/docs/updates.md)
- [Troubleshooting Common Metadata Upload Errors](https://docs.cosmosid.com/v2-0/documentation/technical-appendix/technical-appendix/metadata-errors.md)
- [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.
- [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.
- [EU GDPR Clause ](https://docs.cosmosid.com/docs/technical-appendix/eu-gdpr.md): Description of your new file.
- [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
- [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.
- [FAQ](https://docs.cosmosid.com/docs/technical-appendix/faq.md)
- [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.
- [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 CHAMP](https://docs.cosmosid.com/docs/api-reference/example-running-champ.md)
- [Example: Running 16S Short-Read](https://docs.cosmosid.com/docs/api-reference/upload_16s.md)
- [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)
- [What is Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/About.md)
- [Quickstart](https://docs.cosmosid.com/DAP_docs/quickstart.md): Go from raw omics data to publication-ready figures in your browser, with no code required.
- [Workspaces](https://docs.cosmosid.com/DAP_docs/workspaces.md): The digital counterpart of a microbiome research unit: a virtual space where members of a research team can keep all the assets, omics data, analysis tools and results together.
- [Studies](https://docs.cosmosid.com/DAP_docs/studies.md): A centralized repository for everything related to a research project: ’omics data, sample metadata, analysis projects, results, and the knowledge generated over time.
- [The Study Dashboard](https://docs.cosmosid.com/untitled-page.md): How to navigate all resources and tools inside a study: Analysis Projects, Data Tables, sample metadata, files and running jobs.
- [Importing data into a study](https://docs.cosmosid.com/DAP_docs/importing-data-in-studies.md): Once a Study has been created, it's necessary to import data into it. This page describes the main routes to import data into studies.
- [Exporting Data from Cosmos-Hub Pipelines](https://docs.cosmosid.com/DAP_docs/export-from-cosmos-hub-pipelines.md): This guide walks you through exporting profiled samples from Cosmos-Hub Pipelines and importing them into a Cosmos-Hub 2.0 workspace
- [Create a cohort with Query Builder](https://docs.cosmosid.com/DAP_docs/query-builder.md)
- [Analysis Projects (AP)](https://docs.cosmosid.com/DAP_docs/analysis-project-AP.md): An Analysis Project holds a cohort and every analysis run on it, with each saved result kept as a snapshot.
- [The Analysis Studio](https://docs.cosmosid.com/DAP_docs/analysis-studio.md)
- [Analysis Snapshots](https://docs.cosmosid.com/DAP_docs/analysis-snapshots.md): A snapshot records the state of an Analysis Project at a point in time, including the module, its parameters and the output produced.
- [Overview](https://docs.cosmosid.com/DAP_docs/preprocessing-overview.md)
- [Pre-processing Parameters](https://docs.cosmosid.com/DAP_docs/pre-processing-parameters.md)
- [Impact of Pre-Processing on Analyses ](https://docs.cosmosid.com/DAP_docs/impact-of-pre-processing.md)
- [Rarefaction Overview](https://docs.cosmosid.com/DAP_docs/rarefaction-analysis-overview.md)
- [Rarefaction on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/rarefaction.md)
- [Alpha diversity Overview](https://docs.cosmosid.com/DAP_docs/alpha-diversity-overview.md)
- [Alpha diversity on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/alpha-diversity.md): Run alpha-diversity analysis on Cosmos-Hub 2.0: the outputs it produces, how to read them, and the parameters that shape them.
- [Beta diversity Overview](https://docs.cosmosid.com/DAP_docs/beta-diversity-overview.md): What beta diversity is, why it's useful, and how the analysis turns microbial profiles into distances and ordination plots you can read.
- [Beta diversity on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/beta-diversity-on-the-dap.md): Run beta-diversity analysis in Cosmos-Hub 2.0: the plots and tables it produces, how to read them, and the parameters that shape them.
- [Overview](https://docs.cosmosid.com/DAP_docs/pcaexplorer-overview.md): What Principal Component Analysis does, how it condenses many features into a few axes, and why it's useful for microbiome data.
- [PCA explorer on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/pca-explorer.md)
- [Overview](https://docs.cosmosid.com/DAP_docs/heatmap-overview.md): What a microbiome heatmap shows and the patterns it helps you spot across your whole dataset at a glance.
- [Heatmap on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/heatmaps.md)
- [Overview](https://docs.cosmosid.com/DAP_docs/univariatecomparison-overview.md)
- [Univariate comparison on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/univariate-comparison.md): This page covers how univariate comparison works in Cosmos-Hub 2.0: the outputs it produces, how to read them, and the parameters you can tune. For the method behind it, see the Univariate comparison overview.
- [Overview](https://docs.cosmosid.com/DAP_docs/stackedbarchart-overview.md): What a stacked bar chart shows about microbial composition, and the exploratory questions it helps you answer.
- [Stacked bar charts on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/stacked-bar-charts.md)
- [Overview](https://docs.cosmosid.com/DAP_docs/machinelearning-overview.md): How the ML Regression and Classification modules learn from microbiome data to predict a target, and when to use each.
- [Build ML Classification and Regression models on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/configuring-a-ml-analysis.md): Build Regression or Classification ML models with Cosmos-Hub 2.0
- [ML Classification on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/ml-classification.md)
- [ML Regression on Cosmos-Hub 2.0](https://docs.cosmosid.com/DAP_docs/ml-regression.md)

## Optional

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


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