All functions

alpha_summary

Print summary statistics of alpha level cutoffs

bcbio bcbio.bcbioRnaDataSet bcbio<-

Accessors for the count matrix of a bcbioRnaDataSet object

plot_ma plot_volcano

Differential expression plots

downloads

File downloads

plot_correlation_heatmap plot_gene_heatmap plot_deg_heatmap

Heatmaps

metadata_table

Metadata table

plot_gene

Plot an individual gene

plot_pca

Plot principal component analysis (PCA)

pool_counts pool_dds

Lane-split FASTQ aggregation functions

plot_total_reads plot_mapped_reads plot_mapping_rate plot_genes_detected plot_gene_detection_saturation plot_exonic_mapping_rate plot_intronic_mapping_rate plot_rrna_mapping_rate plot_counts_per_gene plot_count_density plot_gender_markers plot_pca_covariates

Gene-level quality control plots

res_tables

Differential expression results tables

plot_size_distribution plot_mirna_counts plot_srna_clusters

Small RNA-seq quality control plots

tmm_normalize

Trimmed mean of M-values (TMM) normalization

top_tables

Top tables of differential expression results

tpm

Transcripts per million

write_counts

Write gzipped counts