| ComBat | Adjust for batch effects using an empirical Bayes framework |
| ComBat_seq | Adjust for batch effects using an empirical Bayes framework in RNA-seq raw counts |
| empirical.controls | A function for estimating the probability that each gene is an empirical control |
| f.pvalue | A function for quickly calculating f statistic p-values for use in sva |
| fstats | A function for quickly calculating f statistics for use in sva |
| fsva | A function for performing frozen surrogate variable analysis as proposed in Parker, Corrada Bravo and Leek 2013 |
| irwsva.build | A function for estimating surrogate variables by estimating empirical control probes |
| num.sv | A function for calculating the number of surrogate variables to estimate in a model |
| psva | A function for estimating surrogate variables with the two step approach of Leek and Storey 2007 |
| qsva | A function for computing quality surrogate variables (qSVs) |
| read.degradation.matrix | A function for reading in coverage data from degradation-susceptible regions |
| ssva | A function for estimating surrogate variables using a supervised approach |
| sva | sva: a package for removing artifacts from microarray and sequencing data |
| sva.check | A function for post-hoc checking of an sva object to check for degenerate cases. |
| svaseq | A function for estimating surrogate variables for count based RNA-seq data. |
| sva_network | A function to adjust gene expression data before network inference |
| twostepsva.build | A function for estimating surrogate variables with the two step approach of Leek and Storey 2007 |