---
title: "Introduction"
linkTitle: "Introduction"
type: docs
weight: 1
---

*****

## Main functionalities 

Currently, `SPS` includes 3 main functional categories (*Fig 1*): 

 1. Some pre-defined modules ([tabs](#sps-tabs)) include: 
    a. A workbench for designing and configuring data analysis workflows, 
    b. Downstream analysis and visualization tools for RNA-Seq, and 
    c. A space to make quick ggplots. 
 2. A section with user custom tabs: users define their own shiny tabs.  
 3. An image editing tab "Canvas" which allows users to edit plots made from 
    the previous two categories. 

Besides, SPS provides many functions to extend the default Shiny development, like 
more UI components, server functions. Also, SPS has some useful general R ulitlies
like error catching, logging, and more. 

<center id="sps_structure" >
<img src="../img/sps_structure.png" style="height: 500px;"></img>
</center>

**Figure 1.** SPS Features

The framework provides an
interactive web interface for workflow management and data visualization.


## Detailed features 

To know more about SPS features, find your favorite section below and click the link 
below to navigate to the section, or use the left sidebar menu to navigate. 


```{r echo=FALSE}
spsComps::gallery(
    texts = c(
        "App structure",
        "User login",
        "Loading themes",
        "Workflow module",
        "Workflow metadata",
        "Workflow step selection & desgin",
        "Workflow Execution",
        "RNAseq normalization",
        "RNAseq DEG",
        "RNAseq plots",
        "Canvas Module",
        "Admin login",
        "Admin app stats",
        "Admin user control",
        "Customizable notifications",
        "Customizable interactive tutorials",
        "Logging and error handling"
    ),
    hrefs = c(
        "/sps/intro/",
        "/sps/adv_features/login/#main-app-login",
        "/sps/adv_features/login/#main-app-login",
        "/sps/modules/workflow/",
        "/sps/modules/workflow/#2-prepare-a-target-file",
        "/sps/modules/workflow/#3-prepare-a-workflow-file",
        "/sps/modules/workflow/#5-run-or-finish-workflow-preparation",
        "/sps/modules/rnaseq/",
        "/sps/modules/rnaseq/#deg-report",
        "/sps/modules/rnaseq/#plot-options",
        "/sps/canvas/",
        "/sps/adv_features/login/#admin-page",
        "/sps/adv_features/login/#app-information",
        "/sps/adv_features/login/#account-control",
        "/sps/adv_features/notification/",
        "/sps/adv_features/guide/",
        "/sps/adv_features/debug/"

    ),
    images = c(
        "../img/sps_structure.png",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/user_login.png?raw=true",
        "https://systempipe.org/sps/adv_features/login_theme.gif",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/wf_main.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/wf_targets.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/wf_wf.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/wf_run.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/rnaseq_normalize.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/rnaseq_deg.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/rnaseq_heatmap.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/canvas.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/admin_login.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/admin_server_info.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/admin_user_control.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/sps_notification.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/sps_guide.png?raw=true",
        "https://github.com/systemPipeR/systemPipeR.github.io/blob/main/static/sps/img/logging.png?raw=true"
    ),
    title = "SPS Features",
    enlarge = TRUE,
    enlarge_method = "modal",
    image_frame_size = 2,
    target_blank = FALSE
)
```