rsemverse
An R package whose function rsem_read() reads RSEM *.genes.results files listed in a sample table (sample_id, ref) and returns expected counts or TPM as a data frame with one row per gene symbol and one column per sample, using org.Hs.eg.db or org.Mm.eg.db for human or mouse.
Installation
install.packages("BiocManager")
BiocManager::install("DaikiKumakura/rsemverse")
BiocManager::install(c("org.Hs.eg.db", "org.Mm.eg.db"))rsemverse needs R 4.1 or later; install the OrgDb package of the species you use (org.Hs.eg.db for human, org.Mm.eg.db for mouse).
Status
Ensembl version suffixes are removed before the symbol lookup, rows that share a symbol are summed, and genes without a symbol keep their original ID. On six ENCODE K562 RSEM files (59,526 genes each), 36,385 genes received a symbol, 23,141 kept their ID, and the column sums equalled the input (November 10, 2026). R CMD check passes on Linux, macOS and Windows in CI. Not on CRAN or Bioconductor.