code: def make_scrnaseq_object(samples):
      
      local_sitelib = R_sitelib()
      counts_dir = os.path.dirname(dd.get_in_samples(samples, dd.get_combined_counts))
      gtf_file = dd.get_in_samples(samples, dd.get_transcriptome_gtf)
      if not gtf_file:
          gtf_file = dd.get_in_samples(samples, dd.get_gtf_file)
      rda_file = os.path.join(counts_dir, "se.rda")
      if not file_exists(rda_file):
          with file_transaction(rda_file) as tx_out_file:
              rcode = "%s-run.R" % os.path.splitext(rda_file)[0]
              rrna_file = "%s-rrna.txt" % os.path.splitext(rda_file)[0]
              rrna_file = _find_rRNA_genes(gtf_file, rrna_file)
              with open(rcode, "w") as out_handle:
                  out_handle.write(_script.format(**locals()))
              rscript = Rscript_cmd()
              try:
                  # do.run([rscript, "--no-environ", rcode],
                  #        "SingleCellExperiment",
                  #        log_error=False)
                  rda_file = rcode
              except subprocess.CalledProcessError as msg:
                  logger.exception()
docs: load the initial se.rda object using sinclecell-experiment