Package: condiments 1.21.0

Hector Roux de Bezieux

condiments: Differential Topology, Progression and Differentiation

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

Authors:Hector Roux de Bezieux [aut, cre], Koen Van den Berge [aut, ctb], Kelly Street [aut, ctb]

condiments_1.21.0.tar.gz
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condiments_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
condiments/json (API)

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

Bug tracker:https://github.com/hectorrdb/condiments/issues

Datasets:
  • toy_dataset - A toy dataset used in the vignette and in the examples

On BioConductor:condiments-1.21.0(bioc 3.24)condiments-1.20.0(bioc 3.23)

rnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization

6.66 score 32 stars 48 scripts 13 exports 140 dependencies

Last updated from:c90263f07e. Checks:8 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE228
linux-devel-x86_64NOTE473
source / vignettesOK416
linux-release-x86_64NOTE457
macos-release-arm64NOTE312
macos-oldrel-arm64NOTE237
windows-develNOTE511
windows-releaseNOTE448
windows-oldrelNOTE466
wasm-releaseOK218

Exports:create_differential_topologydifferentiationTestfateSelectionTestfateSelectionTest_multipleSamplesimbalance_scoremerge_sdsnLineagesprogressionTestprogressionTest_multipleSamplesslingshot_conditionstopologyTesttopologyTest_multipleSamplesweights_from_pst

Dependencies:abindassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularcaretclasscliclockcodetoolscpp11data.tableDelayedArraydiagramdigestdistinctdoParalleldoRNGdplyrdqrnge1071EcumefarverFNNforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggbeeswarmggplot2ggrepelglobalsgluegowergridExtragtablehardhatigraphipredIRangesirlbaisobanditeratorskernlabKernSmoothlabelinglambda.rlatticelavalifecyclelimmalistenvlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvModelMetricsnlmennetnumDerivparallellypbapplypheatmappillarpkgconfigplyrprincurvepROCprodlimprogressrproxypurrrR6RANNRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressrecipesreshape2rlangrngtoolsrpartRSpectrarsvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoshapeSingleCellExperimentsitmoslingshotsnowSparseArraysparsevctrsspatstat.univarspatstat.utilsSQUAREMstatmodstringistringrSummarizedExperimentsurvivaltibbletidyrtidyselecttimechangetimeDateTrajectoryUtilstransporttzdbutf8uwotvctrsviporviridisviridisLitewithrXVector

Overview of the condiments workflow
Initial pre-processing | Generating a synthetic dataset | Vizualisation | Differential Topology | Exploratory analysis | Trajectory Inference | Differential Progression | Visualization | Testing for differential progression | Differential fate selection | Testing for differential fate selection | Differential Expression | Conclusion | Session Info | References
Rendered fromcondiments.Rmdusingknitr::rmarkdown

Last update: 2021-09-08
Started: 2021-01-26

More controls for the tests used in the condiments workflow
Toy dataset | The topologyTest function | Changing the method or the threshold | Passing arguments to the test method | Using parallelisation | Differential progression and fate selection | Default | Changing the method and / or threshold | Passing more parameters to the test methods | Conclusion | Session Info | References
Rendered fromcontrols.Rmdusingknitr::rmarkdown

Last update: 2021-09-08
Started: 2021-03-01

Generating toy datasets
Rendered fromexamples.Rmdusingknitr::rmarkdown

Last update: 2021-03-01
Started: 2021-03-01

Readme and manuals

Help Manual

Help pageTopics
Create Example functioncreate_differential_topology
Differential differentiationdifferentiationTest
Differential fate selection TestfateSelectionTest fateSelectionTest,matrix-method fateSelectionTest,PseudotimeOrdering-method fateSelectionTest,SingleCellExperiment-method fateSelectionTest,SlingshotDataSet-method
Differential fate selection Test with multiple samplesfateSelectionTest_multipleSamples fateSelectionTest_multipleSamples,matrix-method fateSelectionTest_multipleSamples,PseudotimeOrdering-method fateSelectionTest_multipleSamples,SingleCellExperiment-method fateSelectionTest_multipleSamples,SlingshotDataSet-method
Imbalance Scoreimbalance_score imbalance_score,matrix-method imbalance_score,SingleCellExperiment-method
Merge slingshots datasetsmerge_sds
Number of lineagesnLineages nLineages,PseudotimeOrdering-method nLineages,SingleCellExperiment-method nLineages,SlingshotDataSet-method
Differential Progression TestprogressionTest progressionTest,matrix-method progressionTest,PseudotimeOrdering-method progressionTest,SingleCellExperiment-method progressionTest,SlingshotDataSet-method
Differential Progression Test with multiple samplesprogressionTest_multipleSamples progressionTest_multipleSamples,matrix-method progressionTest_multipleSamples,PseudotimeOrdering-method progressionTest_multipleSamples,SingleCellExperiment-method progressionTest_multipleSamples,SlingshotDataSet-method
Refitting slingshot per conditionslingshot_conditions slingshot_conditions,PseudotimeOrdering-method slingshot_conditions,SingleCellExperiment-method slingshot_conditions,SlingshotDataSet-method
Differential Topology TesttopologyTest topologyTest,PseudotimeOrdering-method topologyTest,SingleCellExperiment-method topologyTest,SlingshotDataSet-method
Differential Topology Test with multiple samplestopologyTest_multipleSamples topologyTest_multipleSamples,PseudotimeOrdering-method topologyTest_multipleSamples,SingleCellExperiment-method topologyTest_multipleSamples,SlingshotDataSet-method
A toy dataset used in the vignette and in the examplestoy_dataset
weights_from_pstweights_from_pst weights_from_pst,data.frame-method weights_from_pst,matrix-method