Buildsnngraph

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August undefined, 2024

WebApr 17, 2024 · In scran: Methods for Single-Cell RNA-Seq Data Analysis. Description Usage Arguments Details Value Default size factor choices Explanation for size factor rescaling Computing p-values Handling uninteresting factors Author(s) See Also Examples. Description. Model the variance of the log-expression profiles for each gene, … Webscran/R/buildSNNGraph.R. #' \linkS4class {SingleCellExperiment}-friendly wrapper around the \code {\link {makeSNNGraph}} and \code {\link {makeKNNGraph}} functions for …

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WebApr 17, 2024 · bootstrapCluster: Assess cluster stability by bootstrapping buildSNNGraph: Build a nearest-neighbor graph cleanSizeFactors: Clean size factors clusterModularity: Compute the cluster-wise modularity clusterPurity: Evaluate cluster purity clusterSNNGraph: Wrappers for graph-based clustering coassignProb: Compute coassignment probabilities … tiff and tif

Cluster-based mutual nearest neighbors correction - GitHub Pages

WebDefines functions .merge_closest_graph .create_rank_matrix .quick_cluster. #' Quick clustering of cells #' #' Cluster similar cells based on their expression profiles, using either log-expression values or ranks. #' #' @param x A numeric count matrix where rows are genes and columns are cells. #' #' Alternatively, a \linkS4class ... Web7.3 Quality control. Cell calling implicitly serves as a QC step to remove libraries with low total counts and number of detected genes. Thus, we will only filter on the mitochondrial proportion. Figure 7.1: Percentage of mitochondrial reads in each cell in each of the 10X PBMC datasets, compared to the total count. WebOct 15, 2024 · The SNN graph is constructed using the buildSNNGraph function in scran, given the input space to use (here, we use the PCA representation calculated above) … tiff and the geysers

buildSNNGraph : Build a nearest-neighbor graph

k argument in buildSNNGraph - Bioconductor

WebFeb 3, 2024 · A graph where nodes are cells and edges represent connections between nearest neighbors. For buildSNNGraph, these edges are weighted by the number of … WebAug 7, 2024 · There's nothing special here. If you have a subpopulation with fewer than k+1 cells, buildSNNGraph() will forcibly construct edges between cells in that subpopulation … the master herbalistWebApr 3, 2024 · 101 lines (88 sloc) 3.64 KB. Raw Blame. .buildSNNGraph <- function ( x, k=10, d=50, transposed=FALSE, subset.row=NULL, BPPARAM= SerialParam ()) # Builds a … the master house antwerpen

"WebAug 8, 2024 · g.jaccard <- buildSNNGraph(sce.pbmc, use.dimred="PCA", type="jaccard") The text was updated successfully, but these errors were encountered: All reactions. … " - Buildsnngraph

Buildsnngraph

MarioniLab/scran: Methods for Single-Cell RNA-Seq Data Analysis

WebDec 29, 2024 · I used this package for my scRNA-seq data analysis, now I wonder if I can use the function "BuildSNNGraph" on my DNA methylome data (data frame: … WebJul 30, 2024 · Adjust number of clusters with scran/buildSNNGraph. I am using fastMMN for batch correction and subsequently buildSNNGraph and cluster_walktrap for …

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WebOct 20, 2024 · \item{k_celltype}{An integer indicates the number of nearest neighbours used in \code{buildSNNGraph} when grouping cells within each batch. Default is 10.} \item{exprsMat_counts}{A gene (row) by cell (column) counts matrix to be adjusted.} \item{cosineNorm}{A logical vector indicates whether cosine normalisation is performed … WebApr 17, 2024 · buildSNNGraph: Build a nearest-neighbor graph; cleanSizeFactors: Clean size factors; clusterModularity: Compute the cluster-wise modularity; clusterPurity: … findMarkers - buildSNNGraph : Build a nearest-neighbor graph doubletCells - buildSNNGraph : Build a nearest-neighbor graph computeSumFactors - buildSNNGraph : Build a nearest-neighbor graph combinePValues - buildSNNGraph : Build a nearest-neighbor graph In scran: Methods for Single-Cell RNA-Seq Data Analysis. Description Usage … buildSNNGraph, for additional arguments to customize the clustering when … combineMarkers - buildSNNGraph : Build a nearest-neighbor graph Details. This function will first fit a non-linear curve of the form y = ax/(1 + bx) where y … pairwiseTTests - buildSNNGraph : Build a nearest-neighbor graph correlatePairs - buildSNNGraph : Build a nearest-neighbor graph

WebFeb 3, 2024 · If a subpopulation in the data has fewer than k+1 observations, buildSNNGraph and buildKNNGraph will forcibly construct edges between observations in that subpopulation and observations in other subpopulations. This increases the risk that the subpopulation will not form its own cluster as it is more interconnected with the rest of the ... WebMar 27, 2024 · And yes, you can set d=NA in buildSNNGraph. ADD COMMENT • link 3.0 years ago Aaron Lun ★ 28k 0. Entering edit mode. FYI, version 1.3.15 supports d=NA in fastMNN, which saves you having to cosine-normalize and transpose the matrices yourself for entry into reducedMNN. ADD REPLY • link 3.0 ...

Web4 buildSNNGraph buildSNNGraph Build a nearest-neighbor graph Description SingleCellExperiment-friendly wrapper around the makeSNNGraph and makeKNNGraph … WebJul 30, 2024 · Increase the number of neighbours used (k) when running buildSNNGraph.This increases the connectivity of the SNN graph and should reduce the number of clusters (i.e., follow the opposite of the advice given in the comments section here).I am surprised that the default k=10 yields too many clusters, though; I can only …

WebDec 29, 2024 · I want to use "BuildSNNGraph" and then "igraph::cluster_walktrap". Is this right? I notice the description says: Build a shared or k-nearest-neighbors graph for cells based on their expression profiles; x: For the ANY method, a matrix-like object containing expression values for each gene (row) in each cell (column). These dimensions can be ...

WebApr 17, 2024 · Value. For calculateSumFactors, a numeric vector of size factors for all cells in x is returned.. For computeSumFactors, an object of class x is returned containing the vector of size factors in sizeFactors(x).. Overview of the deconvolution method. The computeSumFactors function implements the deconvolution strategy (Lun et al., 2016) … the masterixWebAn existing igraph::Graph object, typically built by BuildSNNGraph::Results::to_igraph(). weights: Pointer to an array of weights of length equal to the number of edges in graph. Returns A Results object containing the clustering results for all cells. the mastering projectWebJan 5, 2024 · 2 Method description. The first step is to compute the centroids for each cluster by simply summing the (log-)expression values for all cells in the same cluster. Note that this is done after cosine normalization if cos.norm=TRUE, see the normalization discussion for more details. The second step is to perform a PCA on the centroid … the master jeweler etsyWebBrowse the content of Bioconductor software packages. the master impression minoan creteWebMay 6, 2024 · This time I am trying to figure out how can I determine if I have obtained optimal number of clusters using the buildSNNgraph and igraph approach. I can … the master in frenchWebMar 29, 2024 · buildSNNGraph: Build a nearest-neighbor graph clusterCells: Cluster cells in a SingleCellExperiment combineBlocks: Combine blockwise statistics combineMarkers: Combine pairwise DE results into a marker list combinePValues: Combine p-values combineVar: Combine variance decompositions computeMinRank: Compute the … the mastering show podcastWeb4 buildSNNGraph buildSNNGraph Build a nearest-neighbor graph Description SingleCellExperiment-friendly wrapper around the makeSNNGraph and makeKNNGraph … the mastering academy