bayNormJL.jl: bayNorm in Julia

bayNorm in Julia, super fast! The R package can be found here (more detailed about parameter setting): https://github.com/WT215/bayNorm](https://github.com/WT215/bayNorm).

bayNormJL is a Julia package which is used to normalize single-cell RNA-seq data.

Code for bayNorm paper

The code for producing figures in bayNorm paper [1] can be found here

To install the package under Julia 1.2+ using Pkg, simply enter its interactive mode by pressing ] in the Julia REPL and run add https://github.com/WT215/bayNormJL.jl.git

The output of bayNorm is of type Dict.

Quick start

using bayNormJL

#A toy scRNA-seq data
Data=[1:10 1:10 3:12 4:13] 
#Cell-specific capture efficiency. Default is nothing.
Beta=[0.1,0.5,0.3,0.4]

outt=bayNormJL.bayNorm(Data=Data, BETA_vec=Beta, Conditions = nothing,UMI_sffl = nothing,Prior_type = nothing,mode_version =false,mean_version=true,S = 20,FIX_MU = true,BB_SIZE_par = true, verbose = true)

#Access to the normalized data
outt["Bay_out"]

Parallel computing

using Distributed
#Using 8 cores
addprocs(8)
@everwhere using bayNormJL

#A toy scRNA-seq data
@everywhere Data=[1:10 1:10 3:12 4:13] 
#Cell-specific capture efficiency. Default is nothing.
@everywhere Beta=[0.1,0.5,0.3,0.4]

outt=bayNormJL.bayNorm(Data=Data, BETA_vec=Beta, Conditions = nothing,UMI_sffl = nothing,Prior_type = nothing,mode_version =false,mean_version=true,S = 20,FIX_MU = true,BB_SIZE_par = true, verbose = true)

#Access to the normalized data
outt["Bay_out"]

References

• [1] Tang et al. (2019). Bioinformatics.