README.md

In maximilian-heeg/magieR: Run `magic-impute` on scRNA Seq dataset in R

magieR

An easy to use wrapper to run magic in scRNA-Seq datasets in R. For further information on magic see https://www.krishnaswamylab.org/projects/magic

Installation

magieR can be easily installed from Github using devtools::install():

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("maximilian-heeg/magieR")

Note: Most recently, I needed to install the newest version of reticulate from git. Otherwise I got a lot of segfaults. Also, make sure that the libopenblas from R and in the python environment match. I needed to run the following commands in the basilisk conda environment .cache/basilisk/1.2.0/magieR-0.1.0/env:

conda install nomkl numpy scipy scikit-learn numexpr
conda remove mkl mkl-service
conda install libopenblas=0.3.15 -c conda-forge

See the vignette on how to use the wrapper with Seurat and SingleCellExperiment objects.

maximilian-heeg/magieR documentation built on May 11, 2021, 3:54 a.m.