Analogizer is a package for integrating and analyzing multiple single-cell datasets, developed and maintained by the Macosko lab. It relies on integrative non-negative matrix factorization to identify shared and dataset-specific factors.
Analogizer is written in R and has a few other system requirements (Java) and recommended packages (umap in Python). To install the most recent development version, follow these instructions:
- Install R (>= 3.4)
- Install Rstudio (recommended)
- Make sure you have Java installed in your machine. Check by typing
java -version
into Terminal or CommandPrompt. - Generate an auth token for the Analogizer repo, making sure to include all repo permissions.
- Use the following R commands.
install.packages('devtools')
library(devtools)
install_github('MacoskoLab/Analogizer', auth_token = '<token>')
Installing RcppArmadillo on R>=3.4 requires Clang >= 4 and gfortran-6.1. Follow the instructions below if you have R version 3.4.0-3.4.4. These instructions (using clang4) may also be sufficient for R>=3.5 but for newer versions of R, it's recommended to follow the instructions in this post.
- Install gfortran as suggested here
- Download clang4 from this page
- Uncompress the resulting zip file and type into Terminal (
sudo
if needed):
mv /path/to/clang4/ /usr/local/
- Create
.R/Makevars
file containing following:
# The following statements are required to use the clang4 binary
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/clang4/bin/clang++
CXX11=/usr/local/clang4/bin/clang++
CXX14=/usr/local/clang4/bin/clang++
CXX17=/usr/local/clang4/bin/clang++
CXX1X=/usr/local/clang4/bin/clang++
LDFLAGS=-L/usr/local/clang4/lib
For example, use the following Terminal commands:
cd ~
mkdir .R
cd .R
nano Makevars
Paste in the required text above and save with Ctrl-X
.
For usage examples and guided walkthroughs, check the vignettes
directory of the repo.