all_numeric |
for a vector x, check if all non-NA elements of x can be converted to numeric |
filter_genes |
Filter genes with low counts |
get_gene_id |
Get all gene IDs in a DESeqDataSet for a given gene name. |
make_dds |
Make DESeqDataSet from counts matrix and metadata |
mean_sd_plot |
Create a mean-sd plot Make a scatterplot that shows for each gene its standard deviation versus mean. |
plot_biotypes |
Plot number of counts per sample and biotype |
plot_chromosome |
Plot gene expression along a chromosome |
plot_gene |
Plot a gene |
plot_gene_detection |
Plot number of detected genes for each sample |
plot_library_complexity |
Plot the library complexity |
plot_loadings |
Plot loadings of a principal component |
plot_ma |
MA-plot of a differential testing result |
plot_pca |
Plot results of a principal component analysis |
plot_pca_scatters |
Plot matrix of PCA scatter plots |
plot_sample_clustering |
Plot clustering of samples in a distance heatmap |
plot_sample_MAs |
MA plots of samples |
plot_total_counts |
Plot total counts per sample |
plot_within_level_sample_MAs |
Plot correlations of samples within a level of a group |
save_plots_to_pdf |
Save list of plots to PDF |
T47D |
The T47D cell line data of RNA-seq experiment GSE89888 |
T47D_diff_testing |
Differential expression results corresponding to the T47D data set. |