Package index • rsemflow

Import and storage

read_rsem_study(): Import RSEM gene-level results and metadata
read_study() write_study(): Read and write RSEMflow studies
summarize_study(): Summarize expression-level QC statistics

Expression

normalize_expression(): Normalize or transform expression values
compute_pca(): Compute PCA tables from transformed expression
compute_correlation(): Compute sample correlation

Differential expression

differential_deseq2(): Run metadata-driven DESeq2 differential expression

Gene sets

run_gsea(): Run preranked GSEA
run_gsva(): Run GSVA or ssGSEA pathway scoring

Annotation

annotate_ensembl(): Annotate Ensembl gene IDs using a local Bioconductor OrgDb
annotate_gtf(): Annotate genes from a GTF file

Command line

cli_main(): RSEMflow command-line entry point

Package

rsemflow rsemflow-package: rsemflow: metadata-driven downstream analysis for RSEM