Man pages for StoreyLab/factorial-MA-RS
Draft of factorial manuscript (as a package)
| add_counts | Add counts to the levels of a factor |
| constructPseudoR2 | calculate pseudo-R^2 for every row based on a dispersion... |
| construct_R2s | construct R2 across all conditions |
| do_row | perform an operation on each line of a rowwise data frame |
| geom_sided_violin | a violin plot with two sides |
| inflate | Expand a dataset to include all factorial combinations of one... |
| normalizeMatrix | Normalize an RS/MA matrix according to the appropriate... |
| normalizeMatrix.matrix | Normalize an RNA-Seq matrix |
| pathway | 30 genes involved in biologically relevant pathways |
| perform_edgeR | Perform edgeR exact test on a matrix, given the groups |
| pool_matrix.matrix | Given a microarray/RNASeq matrix and a subset of columns,... |
| pool_matrix.RGList | method for pooling an RGList object |
| prepare_SRA | prepare BioSample metadata for the Short Read Archive upload |
| preprocess | create R datasets that end up in the data/ subdirectory, such... |
| R2s | compute R-squared values for many genes |
