scAlign

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions and batches

Tutorials

Unsupervised alignment and projection of HSCs

Multiway alignment using all pairs method

Supervised/Semi-supervised alignment

Updates

(9/4/2019) Updated install instructions to include Tensorflow for R method..

(5/9/2019) Updated to version 1.0! Tutorials for multiple modes of operation now available.

R Package and Bioconductor

Bioconductor for now will only support the Linux version of scAlign.

The latest version of scAlign for all systems can always be found at github.

install.packages('devtools')
devtools::install_github(repo = 'quon-titative-biology/scAlign')
library(scAlign)

Package requirements

Guide to installing python and Tensorflow on different operating systems.

(Python)

On Windows:

1. Download Python 3.6.8. Note, newer versions of Python (e.g. 3.7) cannot use TensorFlow at this time.
2. Make sure pip is included in the installation.

On Ubuntu:

1. sudo apt update
2. sudo apt install python3-dev python3-pip

On MacOS (homebrew):

1. /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
2. export PATH="/usr/local/bin:/usr/local/sbin:$PATH"
3. brew update
4. brew install python # Python 3

(Tensorflow)

In an R session:

library(tensorflow)
install_tensorflow(version = "gpu") ## Removing version will install CPU version of Tensorflow