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README.Rmd
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README.Rmd
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---
output:
md_document:
variant: markdown_github
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# sake
[](https://travis-ci.com/naikai/sake)
[](https://codecov.io/gh/naikai/sake)
## **S**ingle-cell RNA-Seq **A**nalysis and **K**lustering **E**valuation
The aim of `sake` is to provide a user-friendly tool for easy analysis of NGS Single-Cell transcriptomic data
<img src="vignettes/Figures/SAKE_workflow.png" width="1024px" height="647px" />
**Flowchart of SAKE package and example analysis results**: **a)** Analysis workflow for analyzing single-cell RNA-Seq data. **b)** Quality Controls to compare total sequenced reads to total gene transcripts detected. **c)** Sample correlation heat map plot **d)** A heat map of sample assignment from NMF run, with dark red indicating high confidence in cluster assignments **e)** t-SNE plot to compare NMF assigned groups with t-SNE projections. **f)** A table of NMF identified features (genes defining each cluster) and a box plot of gene expression distributions across NMF assigned groups. **g)** Summary table for GO term enrichment analysis for each NMF assigned group.
## Installation
First we will install some prerequisite libraries before installing `sake`
For **Centos** (tested on 6.9)
``` bash
sudo yum install openssl-devel libcurl-devel libpng-devel libxml2-devel libxslt
# Require `gcc` >= 4.6
sudo yum install centos-release-scl
sudo yum install devtoolset-3-toolchain
scl enable devtoolset-3 bash
```
For **Ubuntu** (tested on 16.10)
``` bash
sudo apt-get install libcurl4-openssl-dev libpng-dev libxslt-dev libssl-dev libxml2-dev xsltproc
```
For **Mac OS** (tested on Sierra 10.12.1)
``` bash
# follow instructions to install brew on MAC
http://brew.sh
# install required packages
brew install curl openssl libpng libxslt libxml2
# update gcc
brew install gcc48
```
#### Download and [Install R](http://cran.wustl.edu)
- Download and [Install Rstudio](https://www.rstudio.com/products/rstudio/download/) (Suggested but not required)
#### To install the latest development version from GitHub (around 30 minutes)
```R
source("http://bioconductor.org/biocLite.R")
biocLite(c("annotate", "AnnotationHub", "biomaRt", "DESeq2", "gage", "gageData", "GO.db", "pathview", "plotly", "DT"))
install.packages("devtools")
devtools::install_github("renozao/pkgmaker", ref="develop")
devtools::install_github("naikai/sake")
```
#### To install the latest development version from [Packrat](https://rstudio.github.io/packrat/) (around 10 minutes)
- Download [file](https://drive.google.com/file/d/1UIAZ6yfWLItJCJYMls3XZ3HzQogKxDBS/view?usp=sharing)
- Unarchive file, open the folder, start `R` in this folder
- Packrat will then automate the whole process for you
## Usage
```R
library(sake)
shiny::runApp(system.file("sake", package="sake"))
```
## Getting Started
Please follow the links to briefly walk you through the functions of `sake` package.
- [Data input](vignettes/Data_Input.Rmd)
- [Quality control](vignettes/Quality_Control.Rmd)
- [Filtering](vignettes/Filtering.Rmd)
- [Run NMF](vignettes/NMF.Rmd)
- [Visualization](vignettes/Visualization.Rmd)
- [DE and Enrichment](vignettes/DE_Enrich.Rmd)
- Example1 - Ting et al [HTML](vignettes/Ting.Rmd) [PDF](vignettes/Ting_pdf.pdf)
- Example2 - Treutlein et al [HTML](vignettes/Treutlein.Rmd) [PDF](vignettes/Treutlein_pdf.pdf)
## Copying & Distribution
Please note that this project is released with a [Contributor Code of Conduct](CONDUCT.md). By participating in this project you agree to abide by its terms.