Construct Benchmarks for Single Cell Analysis Methods

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Documentation for package ‘CellBench’ version 1.20.0

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

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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