# Construct Benchmarks for Single Cell Analysis Methods

## Documentation for package ‘CellBench’ version 1.17.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CellBench-package | A framework for benchmarking combinations of methods in multi-stage pipelines
any_task_errors | Check if any tasks produced errors
any_task_errors.benchmark_tbl | Check if any tasks produced errors
apply_methods | Apply methods
apply_methods.benchmark_tbl | Apply methods
apply_methods.list | Apply methods
apply_methods.tbl_df | Apply methods
apply_metrics | Apply methods
arrow_sep | Unicode arrow separators
as_pipeline_list | convert benchmark_tbl to list
begin_benchmark | Apply methods
cache_method | Create a cached function for CellBench
CellBench | A framework for benchmarking combinations of methods in multi-stage pipelines
cellbench_case_study | Open vignetted containing a case study using CellBench
cellbench_file | Get path to CellBench packaged data
clear_cached_datasets | Clear cached datasets
clear_cellbench_cache | Clear CellBench Cache
collapse_pipeline | Collapse benchmark_tbl into a two column summary
data_list | Constructor for a data list
filter_zero_genes | Filter out zero count genes
fn_arg_seq | Create a list of functions with arguments varying over a sequence
fn_list | Constructor for a function list
is.task_error | Check for task errors
keep_high_count_cells | Filter down to the highest count cells
keep_high_count_genes | Filter down to the highest count genes
keep_high_var_genes | Filter down to the most variable genes
load_all_data | Load CellBench Data
load_cell_mix_data | Load CellBench Data
load_mrna_mix_data | Load CellBench Data
load_sc_data | Load CellBench Data
mhead | Get head of 2 dimensional object as a square block
pipeline_collapse | Collapse benchmark_tbl into a two column summary
sample_cells | Sample cells from a SingleCellExperiment
sample_genes | Sample genes from a SingleCellExperiment
sample_sce_data | This is data for testing functions in CellBench.
set_cellbench_bpparam | Set BiocParallel parameter used CellBench
set_cellbench_cache_path | Set CellBench cache path
set_cellbench_threads | Set number of threads used by CellBench
split_step | Split combined pipeline step
time_methods | Time methods
time_methods.benchmark_timing_tbl | Time methods
time_methods.list | Time methods