Package: condiments 1.13.0

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]

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

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

Peer review:

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-1.13.0(bioc 3.20)condiments-1.12.0(bioc 3.19)

bioconductor-package

13 exports 0.49 score 161 dependencies

Last updated 2 months agofrom:38d7d61dc3

Exports:create_differential_topologydifferentiationTestfateSelectionTestfateSelectionTest_multipleSamplesimbalance_scoremerge_sdsnLineagesprogressionTestprogressionTest_multipleSamplesslingshot_conditionstopologyTesttopologyTest_multipleSamplesweights_from_pst

Dependencies:abindaskpassbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairocaretclasscliclockcodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdiagramdigestdistinctdoParalleldoRNGdplyrdqrnge1071EcumeellipsisfansifarverFNNforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelglobalsgluegowergridExtragtablehardhathttrigraphipredIRangesirlbaisobanditeratorsjsonlitekernlabKernSmoothlabelinglambda.rlatticelavalifecyclelimmalistenvlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeModelMetricsmunsellnlmennetnumDerivopensslparallellypbapplypheatmappillarpkgconfigplyrpngprincurvepROCprodlimprogressrproxypurrrR6raggRANNRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppProgressrecipesreshape2rlangrngtoolsrpartRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmoslingshotsnowSparseArraysparseMatrixStatsspatstat.univarspatstat.utilsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttimechangetimeDateTrajectoryUtilstransporttzdbUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc

Generating toy datasets

Hector Roux de Bézieux

Rendered fromexamples.Rmdusingknitr::rmarkdownon Jun 25 2024.

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

Overview of the condiments workflow

Hector Roux de Bézieux

Rendered fromcondiments.Rmdusingknitr::rmarkdownon Jun 25 2024.

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

More controls for the tests used in the condiments workflow

Hector Roux de Bézieux

Rendered fromcontrols.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2021-09-08
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