rna-timing

Code to run RNA analysis benchmarks

• rna-timing/marker-genes:
  • Calculate Wilcoxon marker genes
  • Requires: datasets/rna-process
  • Produces:
    • {DATA_ROOT}/rna/marker-genes: Marker gene outputs
    • {RESULTS_ROOT}/raw/rna-timing/marker-genes: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/rna-timing/marker-genes
  • Figures: Fig S1d
  • Task summary: 140/155 completed. Total time: 1 day, 14:22:26
    • high_mem_tasks: 10/25 completed. Total time: 0:00:09
• rna-timing/matrix-transpose:
  • Measure the time to swap the storage order of a matrix from cell-major to gene-major
  • Requires: datasets/rna-process
  • Produces:
    • {RESULTS_ROOT}/raw/rna-timing/matrix-transpose: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/rna-timing/matrix-transpose.tsv
  • Figures: Fig S3b
  • Task summary: 100/135 completed. Total time: 5:30:02
• rna-timing/pca-benchmark:
  • Run Normalization + PCA benchmarks
  • Requires: datasets/rna-process
  • Produces:
    • {DATA_ROOT}/rna/pca: PCA coordinate outputs
    • {RESULTS_ROOT}/raw/rna-timing/pca-benchmark: Raw timing outputs
    • {RESULTS_ROOT}/data_tables/rna-timing/pca-benchmark
  • Figures: Fig 1b-d, Fig S1a-c
  • Task summary: 732/850 completed. Total time: 9 days, 12:35:03
    • high_mem_tasks: 25/100 completed. Total time: 3:18:42