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      Fall single cell RNA sequencing workshop @ UCSF

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Introduction and Lectures
Intro to the Workshop and Core
What is Bioinformatics/Genomics Perspective?
Experimental Design and Cost Estimation
Introduction to Command-Line and the Cluster
Logging in and Transferring Files
Intro to Command-Line
Advanced Command-Line (extra)
Running jobs on the Cluster and using modules
Intro to R and Rstudio
Getting Started
Intro to R
Prepare Data in R (extra)
Data in R (extra)
Data Reduction
Project setup
Generating Expression Matrix
scRNAseq Analysis
Prepare scRNAseq Analysis
scRNAseq Analysis - PART1
scRNAseq Analysis - PART2
scRNAseq Analysis - PART3
scRNAseq Analysis - PART4
scRNAseq Analysis - PART5
scRNAseq Analysis - PART6
Guest lecture by Dr. Gerald Quon
Prepare Single Cell Alignment
Single Cell Alignment (scAlign)
Support
Cheat Sheets
Software and Links
Scripts
ETC
Closing thoughts
Workshop Photos
Github
Biocore website

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
---