Package: CellBench 1.29.0

Shian Su

CellBench: Construct Benchmarks for Single Cell Analysis Methods

This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.

Authors:Shian Su [cre, aut], Saskia Freytag [aut], Luyi Tian [aut], Xueyi Dong [aut], Matthew Ritchie [aut], Peter Hickey [ctb], Stuart Lee [ctb]

CellBench_1.29.0.tar.gz
CellBench_1.29.0.zip(r-4.7)CellBench_1.29.0.zip(r-4.6)CellBench_1.29.0.zip(r-4.5)
CellBench_1.29.0.tgz(r-4.6-any)CellBench_1.29.0.tgz(r-4.5-any)
CellBench_1.29.0.tar.gz(r-4.7-any)CellBench_1.29.0.tar.gz(r-4.6-any)
CellBench_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CellBench/json (API)

# Install 'CellBench' in R:
install.packages('CellBench', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shians/cellbench/issues

Datasets:

On BioConductor:CellBench-1.29.0(bioc 3.24)CellBench-1.28.0(bioc 3.23)

softwareinfrastructuresinglecellbenchmarkbioinformatics

9.05 score 33 stars 130 scripts 7 mentions 38 exports 65 dependencies

Last updated from:1afd28752f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR193
linux-devel-x86_64NOTE379
source / vignettesOK259
linux-release-x86_64NOTE436
macos-release-arm64NOTE177
macos-oldrel-arm64NOTE201
windows-develNOTE289
windows-releaseNOTE287
windows-oldrelNOTE277
wasm-releaseOK154

Exports:all_uniqueany_task_errorsapply_methodsapply_metricsarrow_sepas_pipeline_listbegin_benchmarkcache_methodcellbench_case_studycellbench_fileclear_cached_datasetsclear_cellbench_cachecollapse_pipelinedata_listfilter_zero_genesfn_arg_seqfn_listis_all_ofis_one_ofis.task_errorkeep_high_count_cellskeep_high_count_geneskeep_high_var_genesload_all_dataload_cell_mix_dataload_mrna_mix_dataload_sc_datamheadpipeline_collapsesample_cellssample_genesset_cellbench_bpparamset_cellbench_cache_pathset_cellbench_threadssplit_stepstrip_timingtime_methodsunpack_timing

Dependencies:abindaskpassassertthatBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodetoolscpp11curlDBIdbplyrDelayedArraydplyrfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomicRangesgluehttr2IRangeslambda.rlatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoiseopensslpillarpkgconfigpurrrR6rappdirsrlangRSQLiteS4ArraysS4VectorsSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangeutf8vctrswithrXVector

Introduction to CellBench
Introduction | Quick start | Downloading benchmark data | Key objects and concepts | Function piping | Mapping or list-apply | List of datasets | List of functions | Benchmark tibble and list-columns | Applying methods | Advanced usage | Multithreading | Function return caching | Constructing functions with parameter range | Summary
Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2023-02-22
Started: 2018-10-17

Benchmark Data Manipulation
Introduction | Benchmark Tibble | Basics | Operations On Benchmark Tibbles | Operations On list-columns | Unnesting with Lists of data.frames | Manipulating Functions | Basics of Functional Programming | Partial Application | Sequence of Partial Applications | Memoisation | Further Reading
Rendered fromDataManipulation.Rmdusingknitr::rmarkdown

Last update: 2022-10-21
Started: 2018-11-07

Tidyverse Patterns
Introduction | Functional Programming with purrr | Methods as Function Objects | Function Composition | Mapping Over Lists | Table Manipulation with dplyr | Operations on the Benchmark tibble | Calculating multiple columns of metrics | Plotting with ggplot2 | Basic Plotting | Facetting
Rendered fromTidyversePatterns.Rmdusingknitr::rmarkdown

Last update: 2022-10-21
Started: 2019-03-08

Writing Wrappers
Introduction | Wrapper Guidelines | Practical Examples | Simple Wrapper | Final remarks
Rendered fromWritingWrappers.Rmdusingknitr::rmarkdown

Last update: 2019-08-09
Started: 2019-03-29

Timing methods in CellBench
Introduction | Timing methods | Summary
Rendered fromTiming.Rmdusingknitr::rmarkdown

Last update: 2019-02-06
Started: 2019-01-22

Readme and manuals

Help Manual

Help pageTopics
A framework for benchmarking combinations of methods in multi-stage pipelinesCellBench-package CellBench
Check if any tasks produced errorsany_task_errors any_task_errors.benchmark_tbl
Apply methodsapply_methods apply_methods.benchmark_tbl apply_methods.list apply_methods.tbl_df apply_metrics begin_benchmark
Unicode arrow separatorsarrow_sep
convert benchmark_tbl to listas_pipeline_list
Create a cached function for CellBenchcache_method
Open vignetted containing a case study using CellBenchcellbench_case_study
Get path to CellBench packaged datacellbench_file
Clear cached datasetsclear_cached_datasets
Clear CellBench Cacheclear_cellbench_cache
Collapse benchmark_tbl into a two column summarycollapse_pipeline pipeline_collapse
Constructor for a data listdata_list
Filter out zero count genesfilter_zero_genes
Create a list of functions with arguments varying over a sequencefn_arg_seq
Constructor for a function listfn_list
Check for task errorsis.task_error
Filter down to the highest count cellskeep_high_count_cells
Filter down to the highest count geneskeep_high_count_genes
Filter down to the most variable geneskeep_high_var_genes
Load CellBench Dataload_all_data load_cell_mix_data load_mrna_mix_data load_sc_data
Get head of 2 dimensional object as a square blockmhead
Sample cells from a SingleCellExperimentsample_cells
Sample genes from a SingleCellExperimentsample_genes
This is data for testing functions in CellBench.sample_sce_data
Set BiocParallel parameter used CellBenchset_cellbench_bpparam
Set CellBench cache pathset_cellbench_cache_path
Set number of threads used by CellBenchset_cellbench_threads
Split combined pipeline stepsplit_step
Time methodstime_methods time_methods.benchmark_timing_tbl time_methods.list