Package: tradeSeq 1.19.0
Hector Roux de Bezieux
tradeSeq: trajectory-based differential expression analysis for sequencing data
tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
Authors:
tradeSeq_1.19.0.tar.gz
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tradeSeq.pdf |tradeSeq.html✨
tradeSeq/json (API)
NEWS
| # Install 'tradeSeq' in R: |
| install.packages('tradeSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/statomics/tradeseq/issues
- celltype - A vector defining cell types, used in the package vignette.
- countMatrix - A count matrix, used in the package vignette.
- crv - A SlingshotDataset object, used in the package vignette.
- gamList - A list of GAM models, used to demonstrate the various tests.
- sds - A SlingshotDataset object, used in the package unit tests.
On BioConductor:tradeSeq-1.19.0(bioc 3.20)tradeSeq-1.18.0(bioc 3.19)
Last updated 2 months agofrom:e85d386743
Exports:associationTestclusterExpressionPatternsconditionTestdiffEndTestearlyDETestevaluateKfitGAMgetSmootherPvaluesgetSmootherTestStatsnknotspatternTestplot_evalutateK_resultsplotGeneCountplotSmootherspredictCellspredictSmoothstartVsEndTest
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurlDelayedArrayedgeRfansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehttrigraphIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpbapplypillarpkgconfigprincurveR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesSingleCellExperimentslingshotsnowSparseArraystatmodSummarizedExperimentsystibbleTrajectoryUtilsUCSC.utilsutf8vctrsviridisviridisLitewithrXVectorzlibbioc
Working with multiple conditions
Rendered frommultipleConditions.Rmdusingknitr::rmarkdownon Jun 24 2024.Last update: 2020-10-16
Started: 2020-10-16
Using Monocle as input to tradeSeq
Rendered fromMonocle.Rmdusingknitr::rmarkdownon Jun 24 2024.Last update: 2021-07-02
Started: 2020-04-24
Fitting the models and additional control of fitGAM in tradeSeq
Rendered fromfitGAM.Rmdusingknitr::rmarkdownon Jun 24 2024.Last update: 2021-03-30
Started: 2020-04-24
The tradeSeq workflow
Rendered fromtradeSeq.Rmdusingknitr::rmarkdownon Jun 24 2024.Last update: 2021-11-19
Started: 2019-03-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Perform statistical test to check whether gene expression is constant across pseudotime within a lineage | associationTest associationTest,list-method associationTest,SingleCellExperiment-method |
| A vector defining cell types, used in the package vignette. | celltype |
| Cluster gene expression patterns. | clusterExpressionPatterns clusterExpressionPatterns,list-method clusterExpressionPatterns,SingleCellExperiment-method |
| Assess differential expression patterns between conditions within a lineage. | conditionTest conditionTest,SingleCellExperiment-method |
| A count matrix, used in the package vignette. | countMatrix |
| A SlingshotDataset object, used in the package vignette. | crv |
| Perform statistical test to check for DE between final stages of every lineage. | diffEndTest diffEndTest,list-method diffEndTest,SingleCellExperiment-method |
| Perform test of early differences between lineages | earlyDETest earlyDETest,list-method earlyDETest,SingleCellExperiment-method |
| Evaluate the optimal number of knots required for fitGAM. | evaluateK evaluateK,dgCMatrix-method evaluateK,matrix-method evaluateK,SingleCellExperiment-method |
| fitGAM | fitGAM fitGAM,dgCMatrix-method fitGAM,matrix-method fitGAM,SingleCellExperiment-method |
| A list of GAM models, used to demonstrate the various tests. | gamList |
| Get smoother p-value as returned by 'mgcv'. | getSmootherPvalues |
| Get smoother Chi-squared test statistics. | getSmootherTestStats |
| knots | nknots nknots,list-method nknots,SingleCellExperiment-method |
| Assess differential expression pattern between lineages. | patternTest patternTest,list-method patternTest,SingleCellExperiment-method |
| Evaluate an appropriate number of knots. | plot_evalutateK_results |
| Plot gene expression in reduced dimension. | plotGeneCount plotGeneCount,PseudotimeOrdering-method plotGeneCount,SingleCellExperiment-method plotGeneCount,SlingshotDataSet-method |
| Plot the log-transformed counts and the fitted values for a particular gene along all lineages | plotSmoothers plotSmoothers,gam-method plotSmoothers,SingleCellExperiment-method |
| predictCells | predictCells predictCells,list-method predictCells,SingleCellExperiment-method |
| predictSmooth | predictSmooth predictSmooth,list-method predictSmooth,SingleCellExperiment-method |
| A SlingshotDataset object, used in the package unit tests. | sds |
| Perform statistical test to check for DE between starting point and the end stages of every lineage | startVsEndTest startVsEndTest,list-method startVsEndTest,SingleCellExperiment-method |
