Package index • CAIBIrnaseq

Preprocessing

filter_gexp(): Filter Gene Expression Data

normalize_gexp(): Normalize Gene Expression Data

gexp_preprocess(): Pre-process a gene expression matrix to have different gene annotation

rebase_gexp(): Rebase Gene Expression Matrix

fixMarsExcel(): Fix Excel-Corrupted Gene Names

robust_cv(): Robust Coefficient of Variation

highly_variable_genes(): Identify Highly Variable Genes

estimateTPM(): Estimate Transcripts Per Million (TPM)

readsPerMillion(): Normalize Counts to Reads Per Million (RPM)

transcripts_per_million(): Transcripts Per Million (TPM) Calculation

Exploratory Analysis

pca_gexp(): Perform PCA on Gene Expression Data

plot_pca(): Plot PCA Results for Gene Expression Data

cluster_exp(): Cluster Samples Based on Gene Expression

cluster_k_hc(): Hierarchical Clustering with Optional PCA Dimensionality Reduction

cluster_metadata(): Cluster Metadata in Expression Data

Differential Expression Analysis

diffExpAnalysis(): Differential expression analysis (DESeq2 wrapper)

plot_exp_volcano(): Plot Volcano Plot of Differential Expression Results

plot_exp_boxplot(): Plot Expression Boxplot (with validation)

plot_exp_heatmap(): Plot Expression Heatmap

plot_exp_scatter(): Plot Expression Scatter Plot

plot_qc_filters(): Plot QC Filters for Gene Expression Data

plot_venn(): Plot a Venn diagram for two vectors

Pathway Analysis

pathwayAnalysis(): Pathway Analysis

pathwayFGSEA(): Pathway Enrichment Using FGSEA

pathwayORA(): Pathway Over-Representation Analysis (ORA)

score_pathways(): Score Pathways

score_progeny(): Score PROGENy Pathways

get_pathway_df(): Extract pathway scores and metadata from a SummarizedExperiment

get_pathway_genes(): Get Pathway Genes

plot_pathway_dotplot(): Plot Pathway Analysis Results as a Dot Plot

plot_pathway_heatmap(): Plot Pathway Heatmap

plot_pathway_boxplot(): Plot Pathway Boxplot

plot_pathway_scatter(): Plot Pathway Scatter Plot

Microenvironment & Cell-type Scores

mcp_counter(): MCP-counter wrapper for SummarizedExperiment objects

plot_microenv_heatmap(): Plot Microenvironment Heatmap

plot_progeny_heatmap(): Plot Progeny Heatmap

Utilities and Helpers

get_exp_df(): Extract gene expression and sample annotations

get_annotation_collection(): Get Annotation Collection

getEmptyRows(): Get Empty Rows in a Matrix

plt_boxplot(): Boxplot of gene expression by annotation group

plt_heatmap(): Plot Heatmap with Optional Annotations and Customization

plt_scatter(): Scatter plot of gene expression

prep_exp_hm(): Prepare Gene Expression Data for Heatmap Visualization

prep_scoredf_hm(): Prepare Pathway Scores Data Frame for Heatmap

prep_scores_hm(): Prepare Pathway Scores for Heatmap Visualization

read_rnaseq_out(): Read RNA-seq Output from nf-core/rnaseq