Man pages for ShirinG/exprAnalysis
A package for analysing RNA-seq and expression array data
| Allgenes_limma_pw | Output data frame from diff_limma_pw_unfiltered() |
| batch_removal | batch_removal with sva's ComBat() function |
| countmatrix | Randomly generated expression data (raw) |
| DEgenes_pw | Output data frame from diff_limma_pairwise() |
| diff_limma_all | diff_limma_all (from limma functions). |
| diff_limma_pairwise | diff_limma_pairwise (from limma functions). |
| diff_limma_pw_unfiltered | diff_limma_pw_unfiltered (from limma functions). |
| expmatrix | Randomly generated expression data (normalized) |
| exprAnalysis | exprAnalysis: A package for analysing RNA-seq and expression... |
| geneAnnotations | geneAnnotations (with AnnotationDbi). |
| heatmaps | heatmaps (using heatmaps.2 of "gplots"). |
| MEs | Module Eigengenes example data |
| module_eigengene_plot | module_eigengene_plot (from WGCNA output). |
| normalise_eset | normalise_eset (using beadarray). |
| pathview_func | pathview_func (from pathview functions). |
| pca_plot | pca_plot (from pcaGoPromoter functions). |
| pca_plot_enrich | pca_plot_enrich (from pcaGoPromoter functions). |
| quality_control_plots | quality_control_plots (using arrayQualityMetrics). |
| read_bam_to_countmatrix | read_bam_to_countmatrix |
| read_Illumina | read_Illumina (using beadarray). |
| TF_networks | TF_networks. |
| TFs | Transcription factors from mouse and human |
| TFs_paper | Transcription factors from human (published list) |
| var_vs_mean | var_vs_mean |
| wgcna_heatmaps | wgcna_heatmaps (from WGCNA functions). |
| wgcna_modulememberships | wgcna_modulememberships (from WGCNA functions). |
| wgcna_plotDendroAndColors | wgcna_plotDendroAndColors (from WGCNA functions). |
| wgcna_sample_dendrogram | wgcna_sample_dendrogram (from WGCNA functions). |
