All functions

Print summary statistics of alpha level cutoffs

• alpha_summary

Correlation matrix heatmap

• correlation_heatmap

Differentially expressed gene (DEG) heatmap

• deg_heatmap

Import counts

• import_counts

Import a bcbio project data file

• import_file

Import metadata from bcbio run

• import_metadata

Import a bcbio project summary

• import_summary

Load bcbio run

• load_bcbio_run

Melt RNA-Seq count data to long format and log10 transform

• melt_log10

Count density plot

• plot_count_density

Counts per gene plot

• plot_counts_per_gene

Quickly plot principal component analysis (PCA)

• plot_deseq_pca

Exonic mapping rate plot

• plot_exonic_mapping_rate

Graph sexually dimorphic marker genes

• plot_gender_markers

Genes detection saturation plot

• plot_gene_detection_saturation

Plot an individual gene

• plot_gene

Genes detected plot

• plot_genes_detected

Intronic mapping rate plot

• plot_intronic_mapping_rate

Plot MA

• plot_ma

Mapped reads plot

• plot_mapped_reads

Mapping rate plot

• plot_mapping_rate

rRNA contamination mapping rate

• plot_rrna_mapping_rate

Total reads plot

• plot_total_reads

Volcano plot

• plot_volcano

Pool lane split counts

• pool_lane_split_counts

Pool DESeqDataSet counts for technical replicates

• pool_lane_split_dds

Differential expression results tables

• res_tables

Run DAVID analysis

• run_david

Trimmed mean of M-values (TMM) normalization

• tmm_normalize

Print top table

• top_table

Transcripts per million

• tpm