Plotgenecount
WebbAs you can see through the dynverse guidelines app, it’s relatively fast and can detect linear, bifurcating and tree trajectories accurately. Note that it won’t detect any disconnected or cyclic trajectories. That’s why we have to filter out the cells first, so that only the connected clusters are kept. WebbplotGeneCount(crv, counts, gene = "Mpo") plotSmoothers Plot the log-transformed counts and the fitted values for a particular gene along all lineages Description Plot the smoothers estimated by tradeSeq. Usage
Plotgenecount
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Webb2 mars 2024 · 03/02/2024. tradeSeq is an R package that allows analysis of gene expression along trajectories. While it has been developed and applied to single-cell RNA-sequencing (scRNA-seq) data, its applicability extends beyond that, and also allows the analysis of, e.g., single-cell ATAC-seq data along trajectories or bulk RNA-seq time series … Webb1 dec. 2024 · plotGeneCount(exprMatrix) allows to obtain only the plot before building the rankings. Since the rankings are created individually for each cell, in principle, it is …
WebbPackage ‘tradeSeq’ April 8, 2024 Type Package Title trajectory-based differential expression analysis for sequencing data Date 2024-03-17 Version 1.12.0 Webb20 maj 2024 · Dear @hpages,. In the last release we have added support for sparse matrices, so that that is the current expected behaviour. When using dense matrices (as before), the behavior should have not changed, and you can keep using the same code.
Webb5 jan. 2010 · parameters including: counts. The count matrix, genes in rows and cells in columns. Only needed if the input is of the type SlingshotDataSet and the gene argument … Webb25 feb. 2024 · Internally, tradeSeq builds on the mgcv package by fitting additive models using the gam function. The core fitting function, fitGAM, will use cubic splines as basis functions, and it tries to ensure that every lineage will end at a knot point of a smoother. By default, we allow for 6 knots for every lineage, but this can be changed with the ...
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Webb6 mars 2024 · The plotGeneCount also allows you to visualize the trajectory in reduced space, where each cell is colored according to its expression of the gene as defined by … tales n\\u0027clothing vordingborgWebbThese plots can also be produced #' with the function \code{\link{plotGeneCount}}. #' @param nCores Number of cores to use for computation. #' @param verbose Should the function show progress messages? (TRUE / FALSE) #' @param assayName Name of the assay containing the expression matrix (e.g. in \link ... two-bean chilitalesmyth entertainmentWebb14 nov. 2024 · While if the gene set is marker of a high percentage of cells in the dataset (i.e. neurons), the distribution might start approaching the look of a gene-set of … tales my grandmother told meWebb5 jan. 2010 · plotGeneCount() Plot gene expression in reduced dimension. plotSmoothers() Plot the log-transformed counts and the fitted values for a particular gene along all lineages. Data. The dataset used in example. gamList. A list of GAM models, used to demonstrate the various tests. celltype. A vector defining cell types, used in the package … tales not exactly appropriateWebb3 dec. 2024 · The histogram provided by 'AUCell_buildRankings()' allows to quickly check this distribution. 'plotGeneCount(exprMatrix)' allows to obtain only the plot before building the rankings. Value. Quantiles with the number of genes detected by cell (invisible). his result is also printed if verbose=TRUE. tales my lifeWebb13 maj 2024 · The plotGeneCount function plots the cells in reduced dimension, color by gene count for a specified gene, and add lineages. The monocle package already … tales moonlight