iscream benchmarks: (sc)WGBS BED files, regions and results

This repository contains the datasets and results from benchmarking the iscream R package. To run the benchmarks, go to https://github.com/huishenlab/iscream-paper, a repo that contains the code to run benchmarks and produce the figures in the iscream manuscript.

WGBS datasets

The single-cell files (sc_beds.zip) are from the snmC-seq2 paper and were aligned with the BISCUIT aligner. The bulk files (bulk_beds.zip) are from a project in our lab, also aligned with the BISCUIT aligner.)

Information on converting these BED files into bismark BED files can be found at https://github.com/huishenlab/iscream-paper.

methscan_data.zip contains the tabixed coverage BED files from the methscan tutorial used in the "Plotting TSS methylation profiles" iscream vignette.

Regions

genes.bed contains the loci of 20,048 protein coding genes and were used to benchmark iscream's summarize_regions function. canary_dmrs.bed contains over 30,000 regions and were used to benchmark iscream's tabix queries and BSseq object creation.

Results

Benchmarking results are included in benchmark_results.zip.