QC SUMMARIES
obj-qc_ref.rds;obj-qc_sim.rds 

data.frame containing gene-, cell-level, and global quality control (QC) summaries across all references and methods. Specifically, these include:

- datset,subset: reference dataset and subset identifier
- metric: gene-, cell-level, or global quality control summary
- method: simulation method used ('ref' for the non-synthetic reference dataset)
- group: cell grouping used (one of 'global', 'batch', or 'cluster')
- id: cell group identifier, e.g., the batch or cluster annotation ('foo' when 'group' is 'global')
- value: summary value for a given feature (gene-level), cell (global and cell-level), or pair thereof (e.g., correlations)

1/2D STATISTICS
obj-stat_1d.rds;obj-stat_2d.rds

data.frame containing one-/two-dimensional test statistics results across all datasets, methods, and summaries (or relevant pairs thereof). In particular, these comprise:

- method: simulation method used to generate the data
- stat1/2d: test statistic used for comparing reference and simulation summary (or summaries) ('ks(2)' for (2D) Kolmogorov-Smirnov, 'ws' for Wasserstein metric, 'emd' for earth mover's distance)
- datset,subset: reference dataset and subset identifier
- metric(1/2): gene-, cell-level, or global quality control summary (or summaries)
- group: cell grouping used (one of 'global', 'batch', or 'cluster')
- id: cell group identifier, e.g., the batch or cluster annotation ('foo' when 'group' is 'global')
- stat: value of the test statistic

INETGRATION RESULTS
obj-batch_res.rds

data.frame containing integration results for reference and simulated data across all type 'b' datasets and methods, and integration methods. Specifically, it includes the following columns:

- datset,subset: reference dataset and subset identifier
- method: simulation method used ('ref' for the non-synthetic reference dataset)
- batch_method: integration method used to correct for batch effects
- batch: ground-truth cell batch label
- ldf,cms: cell-specific difference in local density factor and mixing score

CLUSTERING RESULTS
obj-clust_res.rds

data.frame containing clustering results for reference and simulated data across all type 'k' datasets and methods, and clustering methods. Specifically, it includes the following columns:

- datset,subset: reference dataset and subset identifier
- method: simulation method used ('ref' for the non-synthetic reference dataset)
- clust_method: clustering method used to predict cell cluster assignments
- cluster: ground-truth cell cluster annotation
- pr,re,F1: cluster-level precision, recall, and F1 score

RUNTIMES
obj-rts.rds

data.frame containing timings of parameter estimation and data simulation across all methods, and 5 replicates each for various random gene- and cell-subsets of one dataset per type. It includes: 

- method: simulation method used 
- datset,subset: reference dataset and subset identifier
- reftyp: reference dataset type (one of 'n', 'b', 'k', or 'g')
- ngs,ncs: number of genes/cells samples ('NA' if no downsampling)
- est,sim: runtime (in seconds) for parameters estimation and data simulation ('Inf' when estimation/simulation failed, 'est' is 'NA' when there is no separate estimation step)

SESSION INFO
session_info.txt

capture of sessionInfo()'s output upon loading all libraries used throughout the Snakemake workflow.