# Mantle

## Docs

- [Database](https://docs.mantlebio.com/features/database.md)
- [Compute environment](https://docs.mantlebio.com/features/notebooks/environment.md)
- [Intro to Mantle Notebooks](https://docs.mantlebio.com/features/notebooks/introduction.md)
- [Pipelines](https://docs.mantlebio.com/features/pipelines.md)
- [AWS](https://docs.mantlebio.com/integrations/aws.md)
- [Benchling](https://docs.mantlebio.com/integrations/benchling.md)
- [GitHub](https://docs.mantlebio.com/integrations/github.md)
- [Nextflow](https://docs.mantlebio.com/integrations/nextflow.md)
- [Intro to Mantle](https://docs.mantlebio.com/introduction.md)
- [Interact with your Mantle Database](https://docs.mantlebio.com/sdk/datasets.md)
- [FAQ](https://docs.mantlebio.com/sdk/faq.md)
- [Interact with Mantle programmatically using the Mantle SDK](https://docs.mantlebio.com/sdk/introduction.md)
- [Interact with Mantle Pipeline runs](https://docs.mantlebio.com/sdk/pipeline_runs.md)
- [Welcome](https://docs.mantlebio.com/welcome.md)
- [Differential gene expression from bulk RNAseq using Scanpy on Mantle](https://docs.mantlebio.com/workflows/bulk_rnaseq_analysis_scanpy.md)
- [Bulk RNA sequencing data processing with the nf-core rnaseq pipeline on Mantle](https://docs.mantlebio.com/workflows/bulk_rnaseq_processing.md)
- [Tracking single cells in time-lapse microscopy image sequences using SC-Track](https://docs.mantlebio.com/workflows/cell_tracking.md)
- [Cellular segmentation from fluorescence microscopy images using Cellpose on Mantle](https://docs.mantlebio.com/workflows/cellpose_segmentation_processing.md)
- [Running CellProfiler pipelines on Mantle](https://docs.mantlebio.com/workflows/cellprofiler.md)
- [Beyond Matplotlib -- Declarative plotting in Python](https://docs.mantlebio.com/workflows/declarative_plotting.md)
- [Demultiplexing Element AVITI base calls with the Bases2Fastq pipeline on Mantle](https://docs.mantlebio.com/workflows/element_bases_processing.md)
- [Fluorescence quantification after image segmentation using Cellpose](https://docs.mantlebio.com/workflows/fluorescence_quantification.md)
- [Home](https://docs.mantlebio.com/workflows/home.md)
- [Parsing a flow cytometry FCS file using FCSparser](https://docs.mantlebio.com/workflows/parse_fcs_files.md)
- [10x Genomics Visium spatial transcriptomics data processing with the spaceranger count pipeline on Mantle](https://docs.mantlebio.com/workflows/visium_spatial_transcriptomics_processing.md)
- [Visualizing results from Visium spatial transcriptomics with Scanpy on Mantle](https://docs.mantlebio.com/workflows/visium_visualizations.md)
- [Displaying a series of images interactively using Holoviews](https://docs.mantlebio.com/workflows/visualizing_image_series.md)

## OpenAPI Specs

- [openapi](https://docs.mantlebio.com/api-reference/openapi.json)

## Optional

- [Workflows Gallery](https://mantlebio.com/workflows)