All functions

aggregate_replicates

Aggregate lane-split technical replicates

alpha_summary

Print summary statistics of alpha level cutoffs

bcbio bcbio<-

bcbioRNADataSet object accessors

bcbioRNADataSet

bcbioRnaseq

counts

Count matrix accessors

downloads

File downloads for RMarkdown templates

gene2symbol

Gene identifier to symbol conversion

load_run

Load bcbio-nextgen run

melt_log10

Melt count matrix to long format and log10 transform

metadata_table

Metadata table

metrics

Sample metrics

plot_correlation_heatmap

Correlation heatmap

plot_dispersion

Plot dispersion estimates

plot_gender_markers

Plot sexually dimorphic gender markers

plot_gene_heatmap plot_deg_heatmap

Gene heatmap

plot_gene

Plot an individual gene

plot_ma

MA-plot from base means and log fold changes

plot_mean_sd

Plot row standard deviations versus row means

plot_pattern

Make groups of genes using expression profile

plot_pca_covariates

Find correlation between principal components (PCs) and covariates.

plot_pca

Sample PCA plot for transformed data

plot_volcano

Volcano plot

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

Quality control metrics plots

plot_size_distribution plot_mirna_counts plot_srna_clusters

Small RNA-seq quality control plots

results_tables

Differential expression results tables

sample_dirs

Sample directories

tmm

Trimmed mean of M-values (TMM) normalization

top_tables

Top tables of differential expression results

tpm

Transcripts per million (TPM)

txi

tximport list accessor