# Single-cell RNA sequencing data normalization

## Documentation for package ‘bayNorm’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

AdjustSIZE_fun | Adjust MME size estimate
asMatrix | Rcpp version: as.matrix
as_matrix | Rcpp version's as.matrix
bayNorm | A wrapper function of prior estimation and bayNorm function
bayNorm_sup | bayNorm with estimated parameters as input
BB_Fun | Estimating size for each gene by either 1D or 2D maximization of marginal distribution
BetaFun | Estimate capture efficiency for cells
Check_input | Check input
DownSampling | Binomial downsampling
EstPrior | Estimate size and mu for Negative Binomial distribution for each gene using MME method
EstPrior_rcpp | Estimate size and mu for Negative Binomial distribution for each gene using MME method (Rcpp version)
EstPrior_sprcpp | Estimate size and mu for Negative Binomial distribution for each gene using MME method (Rcpp version, sp_mat)
EXAMPLE_DATA_list | A subset of Grun et al (2014) data: 2i samples
NOISY_FUN | Noisy gene detection
noisy_gene_detection | A wrapper function for noisy gene detection from raw data. his produces synthetic control, performs bayNorm on both real cell data and synthetic controls and does noisy gene detection.
Prior_fun | A wrapper function of 'EstPrior' and 'AdjustSIZE_fun'
SyntheticControl | Generate synthetic control
t_sp | Transpose of sparse matrix