Package: CellBench 1.23.0

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]

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CellBench.pdf |CellBench.html✨
CellBench/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:CellBench-1.23.0(bioc 3.21)CellBench-1.22.0(bioc 3.20)

softwareinfrastructuresinglecellbenchmarkbioinformatics

8.68 score 29 stars 95 scripts 248 downloads 7 mentions 38 exports 73 dependencies

Last updated 25 days agofrom:65e4041d27. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxWARNINGNov 18 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macWARNINGNov 19 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macWARNINGNov 18 2024

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:abindaskpassassertthatBHBiobaseBiocFileCacheBiocGenericsBiocParallelbitbit64blobcachemclicodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrfansifastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclelubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplogrpurrrR6rappdirsrlangRSQLiteS4ArraysS4VectorsSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttimechangeUCSC.utilsutf8vctrswithrXVectorzlibbioc

Benchmark Data Manipulation

Shian Su

Rendered fromDataManipulation.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Introduction to CellBench

Shian Su

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Tidyverse Patterns

Shian Su

Rendered fromTidyversePatterns.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Timing methods in CellBench

Shian Su

Rendered fromTiming.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

Writing Wrappers

Shian Su

Rendered fromWritingWrappers.Rmdusingknitr::rmarkdownon Nov 18 2024.

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

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