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). |
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