Package index

Example Data

Load an example simulated SummarizedExperiment object

example_se

Example SummarizedExperiment for testing

Determining the Minimal Gene Threshold

Use to determine which gene should not be included in analysis.

determine_filter_threshold()

Evaluates how pre-filtering thresholds affect the number of discoveries, helping users select an informed minimum count.

Filter Low Expression Genes

Pick a threshold to filter genes with low expression counts

filter_low_exp_genes()

Filter genes with low expression

Run DESeq2 Analysis

Run differential gene expression analysis

run_DESeq2()

Preform Differential Gene Analysis

Shrink Results

To get more reilable estimates run the log2_shrinkage function on DESeq2 results

log2_shrinkage()

Apply log2fold-change shrinkage for more reliable effect-size estimates

Interpret Gene Regulation

Tabularly visualize the number for up and down regulated and insignificant genes

gene_regulation_summary()

Summarize the number of significant, upregulated, and downregulated genes at given thresholds

Visualize Expression

Visualize the gene expression in a volcano plot

generate_volcano()

Visualize results as a volcano plot

Export Results

Export the results of generate_volcano, determine_filter_threshold, log2_shrinkage, and gene_regulation_summary into your working directory.

export_outputs()

Export differential expression results, summary counts, and filtering diagnostics to TSV files