streamRWrapper

Wraps Python3 functions into R commands so that people can run STREAM based single-cell analysis in R and do anything else they like.

Prerequisites

STREAM installation

reference link: https://github.com/pinellolab/STREAM
Since there might be a conflict between Anaconda3 based environment VS computation cluster pre-installed modules, here two approaches to the installation are provided. If you work with R from Anaconda3, install STREAM with conda, elif you work with pre-installed R module, you might need to go for the manual pip installation.

Installation with Anaconda3

$ conda config --add channels defaults
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
$ conda create -n STREAM python=3.6 stream jupyter
$ conda activate STREAM

Conda free installation

Before this, make sure you check which python and which pip which are supposed to show you the path of the pre-installed modules.

git clone https://github.com/pinellolab/STREAM.git
cd STREAM
python setup.py install --user
pip install -r pip_requirements.txt --user

One thing that was terribly annoying is the changing argument naming in the dependency networkx. By default, STREAM requires networkx 2.1 (You can see this when installing from conda). However, in my preinstalled environment, networkx is under version 2.3, where there are different argument naming for equivalent values. The version of your networkx can be checked by running in bash command

pip list | grep networkx

If so, I've got the solution. Run bash commands in the stream git repo directory you just cloned before you install STREAM.

cp PATH/TO/THIS/REPO/STREAM_diff.patch ./
git apply STREAM_diff.patch

The most possible missing packages are listed in pip_requirements.txt, but there can also be other missing ones for different users. You might need to install them by yourself.
After these, try import STREAM from Python to check if the installation is done.

import stream as st

If there is R shared library not found issue, try echo $LD_LIBRARY_PATH to see if the R shared library path is appended in your system. If not, append it.

LD_LIBRARY_PATH=PATH/TO/R/lib:$LD_LIBRARY_PATH

Besides, there are also some additional R packages needed for STREAM to work.

if(!require("devtools")){
    install.packages("devtools")
}
devtools::install_github("Albluca/distutils")
devtools::install_github("Albluca/ElPiGraph.R")

Installation

In R, install the package from this repository with devtools:

library(devtools)
install_github('mvfki/streamRWrapper')

Note that this would only work when I set the repo to public.

Features

In examplePipeline.R, there are the commands to load the necessary environment, a pipeline for testData_real/ that follows the STREAM suggestions, and functions such as one for converting an Python AnnData object to R's SingleCellExperiment object which is widely used. All the functions can be installed with packaging.

mvfki / streamRWrapper