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Muscle : semi-non negative joint decomposition of multiple single cell tensors

Muscle diagram

Muscle Usage

1. Preparation

First of all, before cloning the muscle github package, go to the right directory that you would like to implement Muscle. In the cmd terminal, do

cd {Muscle directory}

then go on to the next step. {Muscle directory} could be /Users/kp223/Muscle.

1. Repository clone

For cloning the github repository, again on the cmd terminal, run the linux code

git clone https://github.com/keleslab/Muscle.git

For R, we need the requirements as below :

  • R: R installation (>=4.2.1)
  • parallel (Not required, but highly recommended for faster implementation)

2. Install/load required R packages

In R, run those codes that download the required packages for running Muscle.

install.packages('pacman')
pacman::p_load(MASS,Matrix,dplyr,rTensor,reshape2,Rcpp,RcppArmadillo,foreach,inline,furrr,purrr,parallel,doParallel,RSpectra,qs,gtools)

Details about implementing codes can be found in the Wiki page of this github. For the users with low memory or the users who wants to just check if Muscle works, we recommend to first try this Li et al 2019 data tutorial.

In case you are already done with installing Muscle, you can direclty move onto section 2 of each of the Wiki pages.