---
title: "Introduction to singleCellTK"
author:
- name: Yichen Wang
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
- name: Irzam Sarfraz
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA  
- name: Rui Hong
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Yusuke Koga
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Salam Abdullatif
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
- name: David Jenkins
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Vidya Akavoor
  affiliation: 
  - Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA
- name: Xinyun Cao
  affiliation: 
  - Rafik B. Hariri Institute for Computing and Computational Science and Engineering, Boston University, Boston, MA
- name: Shruthi Bandyadka
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Anastasia Leshchyk
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Tyler Faits
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Mohammed Muzamil Khan
  affiliation:
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Zhe Wang
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: W. Evan Johnson
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
- name: Joshua D. Campbell
  affiliation: 
  - The Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
  - Program in Bioinformatics, Boston University, Boston, MA
  email: camp@bu.edu  
  
  



package: singleCellTK
output: 
  BiocStyle::html_document:
    toc_float: false
vignette: >
  %\VignetteIndexEntry{1. Introduction to singleCellTK}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

The Single Cell Toolkit (SCTK) is an interactive scRNA-Seq analysis package that
allows a user to upload raw scRNA-Seq count matrices and perform downstream
scRNA-Seq analysis interactively through a web interface, or through a set of
R functions through the command line. The package is written in R with a
graphical user interface (GUI) written in Shiny. Users can perform analysis with
modules for conducting quality control, clustering, batch correction, differential
expression, pathway enrichment, and sample size calculator, all in a simple to
use point and click interface. The toolkit also supports command line data
processing, and results can be loaded into the GUI for additional exploration
and downstream analysis.

# Vignettes

Due to the range of features that are available in SCTK, we have prepared several 
vignettes to help you get started, which are all available at [https://www.camplab.net/sctk/](https://www.camplab.net/sctk/)

# Session info {.unnumbered}

```{r sessionInfo, echo=FALSE}
sessionInfo()
```