wt215 / baynormjl.jl

bayNorm in Julia.

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.

baynormjl.jl's Issues

What is the recommended workflow for reading data?

Thanks for providing this Julia package. I'm struggling with the lack of documentation. What is the recommended way to feed in data? For example, if I have a SingleCellExperiment object in an .rds file, is there a way to read this into Julia or should I convert it into something else in R first, and if so what?