Package: condiments 1.15.0
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:
condiments_1.15.0.tar.gz
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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')) |
Bug tracker:https://github.com/hectorrdb/condiments/issues
- toy_dataset - A toy dataset used in the vignette and in the examples
On BioConductor:condiments-1.13.1(bioc 3.20)condiments-1.12.0(bioc 3.19)
rnaseqsequencingsoftwaresinglecelltranscriptomicsmultiplecomparisonvisualization
Last updated 23 days agofrom:4fa4c3a0f4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:create_differential_topologydifferentiationTestfateSelectionTestfateSelectionTest_multipleSamplesimbalance_scoremerge_sdsnLineagesprogressionTestprogressionTest_multipleSamplesslingshot_conditionstopologyTesttopologyTest_multipleSamplesweights_from_pst
Dependencies:abindaskpassassortheadbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularCairocaretclasscliclockcodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydiagramdigestdistinctdoParalleldoRNGdplyrdqrnge1071EcumefansifarverFNNforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelglobalsgluegowergridExtragtablehardhathttrigraphipredIRangesirlbaisobanditeratorsjsonlitekernlabKernSmoothlabelinglambda.rlatticelavalifecyclelimmalistenvlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeModelMetricsmunsellnlmennetnumDerivopensslparallellypbapplypheatmappillarpkgconfigplyrpngprincurvepROCprodlimprogressrproxypurrrR6raggRANNRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressrecipesreshape2rlangrngtoolsrpartRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscaterscuttleshapeSingleCellExperimentsitmoslingshotsnowSparseArrayspatstat.univarspatstat.utilsSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttimechangetimeDateTrajectoryUtilstransporttzdbUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrXVectorzlibbioc
Generating toy datasets
Rendered fromexamples.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2021-03-01
Started: 2021-03-01
Overview of the condiments workflow
Rendered fromcondiments.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2021-09-08
Started: 2021-01-26
More controls for the tests used in the condiments workflow
Rendered fromcontrols.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2021-09-08
Started: 2021-03-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Create Example function | create_differential_topology |
| Differential differentiation | differentiationTest |
| Differential fate selection Test | fateSelectionTest fateSelectionTest,matrix-method fateSelectionTest,PseudotimeOrdering-method fateSelectionTest,SingleCellExperiment-method fateSelectionTest,SlingshotDataSet-method |
| Differential fate selection Test with multiple samples | fateSelectionTest_multipleSamples fateSelectionTest_multipleSamples,matrix-method fateSelectionTest_multipleSamples,PseudotimeOrdering-method fateSelectionTest_multipleSamples,SingleCellExperiment-method fateSelectionTest_multipleSamples,SlingshotDataSet-method |
| Imbalance Score | imbalance_score imbalance_score,matrix-method imbalance_score,SingleCellExperiment-method |
| Merge slingshots datasets | merge_sds |
| Number of lineages | nLineages nLineages,PseudotimeOrdering-method nLineages,SingleCellExperiment-method nLineages,SlingshotDataSet-method |
| Differential Progression Test | progressionTest progressionTest,matrix-method progressionTest,PseudotimeOrdering-method progressionTest,SingleCellExperiment-method progressionTest,SlingshotDataSet-method |
| Differential Progression Test with multiple samples | progressionTest_multipleSamples progressionTest_multipleSamples,matrix-method progressionTest_multipleSamples,PseudotimeOrdering-method progressionTest_multipleSamples,SingleCellExperiment-method progressionTest_multipleSamples,SlingshotDataSet-method |
| Refitting slingshot per condition | slingshot_conditions slingshot_conditions,PseudotimeOrdering-method slingshot_conditions,SingleCellExperiment-method slingshot_conditions,SlingshotDataSet-method |
| Differential Topology Test | topologyTest topologyTest,PseudotimeOrdering-method topologyTest,SingleCellExperiment-method topologyTest,SlingshotDataSet-method |
| Differential Topology Test with multiple samples | topologyTest_multipleSamples topologyTest_multipleSamples,PseudotimeOrdering-method topologyTest_multipleSamples,SingleCellExperiment-method topologyTest_multipleSamples,SlingshotDataSet-method |
| A toy dataset used in the vignette and in the examples | toy_dataset |
| weights_from_pst | weights_from_pst weights_from_pst,data.frame-method weights_from_pst,matrix-method |
