index.qmd

---
title: "OpenPipelines"
subtitle: |
  OpenPipelines: Best-Practice Workflows for Single-Cell Multi-Omics Analysis

  [Get started](/user_guide){class="btn btn-primary"}
  [Our approach](/fundamentals/concepts){class="btn btn-primary"}
sidebar: false
page-layout: full
title-block-banner: "#f0f5f5"
title-block-banner-color: "#00cc99"
listing:
  - id: fundamentals
    type: default
    template: templates/bullet_listing.ejs
    contents: fundamentals
  - id: user_guide
    type: default
    template: templates/bullet_listing.ejs
    contents: user_guide
  - id: contributing
    type: default
    template: templates/bullet_listing.ejs
    contents: contributing
  - id: more_information
    type: default
    template: templates/bullet_listing.ejs
    contents: more_information
toc: false
---

```{r eval=FALSE, include=FALSE}
library(rmarkdown)
library(languageserver)
```


## Key features

::::{layout-ncol=3}

:::{.card}
#### Modular

Reusable components built with Viash for flexible pipeline construction.

<!--OpenPipelines employs a modular design where individual components are built using Viash, enabling reusability and flexibility in constructing pipelines.-->
:::

:::{.card}
#### Scalable

Leverage Nextflow for execution on various platforms (local, cloud, HPC).

<!-- Leveraging Nextflow, OpenPipelines allows for scalable execution of pipelines on various platforms, including local machines, AWS Batch, Google Cloud Batch, and HPC clusters.-->
:::

:::{.card}
#### Reproducible

Containerized components and unit testing ensure reliable analyses.

<!--By unit testing and containerizing each individual component, OpenPipelines ensures reproducibility of analyses.-->
:::


:::{.card}
#### Collaborative

A framework for sharing and integrating components to foster teamwork.

<!--OpenPipelines fosters collaboration by providing a framework for sharing and integrating components.-->
:::


:::{.card}
#### Living Best Practices

Adapts to evolving single-cell analysis by incorporating current best practices and novel methods.

<!--OpenPipelines adapts to the evolving landscape of single-cell analysis by incorporating living [sc-best-practices](https://sc-best-practices.org) and leveraging novel computational methods from [openproblems.bio](https://openproblems.bio).-->
:::

:::{.card}
#### Multimodal

Supports diverse single-cell data types (RNA, protein, VDJ, ATAC) for multi-omics analyses.

<!--OpenPipelines supports various single-cell modalities, including transcriptomics, proteomics, immunomics, and epigenomics data, enabling comprehensive multi-omics analyses.-->
:::

::::

:::{.alt-background}
## Overview

```{mermaid}
%%| classes: lightbox
flowchart LR
  %% Ingestion
  subgraph ingestion[Step 1: Ingestion]
    direction LR
    10x_ingestion[10x Ingestion]:::subwf
    bd_ingestion[BD Rhapsody\nIngestion]:::subwf
    own_h5mu[Own H5MU]:::subwf
  end
  ingestion:::info

  %% Process samples
  subgraph process_samples[Step 2: Process Samples]
    direction LR
    gex[GEX]:::subwf
    atac[ATAC]:::subwf
    adt[ADT]:::subwf
    vdj[VDJ]:::subwf
    other[Other]:::subwf
  end
  process_samples:::info

  %% Integration and downstream
  subgraph integration[Step 3: Integration]
    direction LR
    harmony[Harmony]:::subwf
    scvi[scVI]:::subwf
    scanvi[scanVI]:::subwf
    etc[...]:::subwf
  end
  integration[Integration]:::info
  
  subgraph downstream[Step 4: Downstream]
    direction LR
    celltype_annotation[Cell Type\nAnnotation]:::subwf
    markergenes[Marker Genes\nAnalysis]:::subwf
    differential[Differential\nExpression]:::subwf
    gene_signature_analysis[Gene Signature\nAnalysis]:::subwf
    ccc[Cell-Cell\nCommunication]:::subwf
  end

  ingestion --> process_samples --> integration --> downstream

  classDef wf fill:#f0f0f0,stroke:#525252
  classDef subwf fill:#d9d9d9,stroke:#525252
  classDef info fill:#f0f0f0,stroke:#525252,stroke-dasharray: 4 4
```


:::

## Getting Started

::::{layout-nrow=1}

:::{.column}
:::{#fundamentals}
:::
:::

:::{.column}
:::{#user_guide}
:::
:::

:::{.column}
:::{#contributing}
:::
:::

:::{.column}
:::{#more_information}
:::
:::

::::