Alignment lecture by Dr. Gerald Quon
Install Python 3.6.8 from here:
https://www.python.org/downloads/release/python-368/
Set some options and make sure the packages cowplot, circlize, tensorflow, scAlign are installed (if not install it), and then load them and verify they all loaded correctly.
In the R console run the following commands
if (!any(rownames(installed.packages()) == "cowplot")){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cowplot")
}
library(cowplot)
if (!any(rownames(installed.packages()) == "circlize")){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("circlize")
}
library(circlize)
if (!any(rownames(installed.packages()) == "ComplexHeatmap")){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")
}
library(ComplexHeatmap)
## if you have conda installed you may need to install tensorflow and initialize your environment fist.
## conda install tensorflow
## reticulate::use_condaenv("anaconda3",required = TRUE)
## reticulate::py_discover_config("tensorflow")
if (!any(rownames(installed.packages()) == "tensorflow")){
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tensorflow")
}
library(tensorflow)
## installs CPU version of TensorFlow Python package, use this if you don't have a GPU.
install_tensorflow(version='1.15rc2')
#install scAlign
if (!any(rownames(installed.packages()) == "scAlign")){
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github(repo = 'quon-titative-biology/scAlign')
}
library(scAlign)
sessionInfo()
Download the template Markdown workshop document PART1 and open it.
In the R console run the following command
download.file("https://raw.githubusercontent.com/ucdavis-bioinformatics-training/2019-Fall-single-cell-RNA-sequencing-Workshop-UCSF/master/scrnaseq_analysis/scRNA_Workshop-alignment.Rmd", "scRNA_Workshop-alignment.Rmd")
Edit the file YAML portion
The top YAML (YAML ain’t markup language) portion of the doc tells RStudio how to parse the document.
---
title: "Single Cell RNAseq Alignment"
author: your_name
date: current_date
output:
html_notebook: default
html_document: default
---