WebbHere, we will look at how Seurat and Signac can be used to integrate scATAC-seq and scRNA-seq data. This exercise is based on this and this tutorial, using data on human peripheral blood mononuclear cells (PBMCs) provided by 10x Genomics. We will use data that have already been pre-processed using CellRanger. WebbrunChromVAR: Estimate Motif Variability Using ChromVAR; runCluster: Find Clusters Using Louvain/Leiden Algorithm; runDiffusionMaps: Dimentionality Reduction by Diffusion …
runChromVAR : Estimate Motif Variability Using ChromVAR
WebbValue. chromVARDeviations-class, which inherits from SummarizedExperiment, and has two assays: deviations and deviation scores.. Details. multiprocessing using bplapply. … WebbAccessiblePeaks: Accessible peaks AddChromatinModule: Add chromatin module AddMotifs: Add DNA sequence motif information AggregateTiles: Quantify aggregated genome tiles AlleleFreq: Compute allele frequencies per cell Annotation: Annotation AnnotationPlot: Plot gene annotations as.ChromatinAssay: Convert objects to a … minigun peashooter
runChromVAR() error: Error in isVirtualExt(exti) : · Issue #211 ...
Webb25 mars 2024 · Calls: RunChromVAR ... bploop.lapply -> .send_to -> .send_to -> -> mcexit That make me confused, and i don't know what it make for this problem. Thanks. The … Webb29 mars 2024 · addBmatToSnap: Add cell-by-bin matrix addGmatToSnap: Add cell-by-gene matrix addPmatToSnap: Add cell-by-peak matrix barcodeInSnapFile: Check barcode existance in snap file boxPlotFeature: Feature Enrichment Boxplot calBmatCor: Check correlation of cell-by-bin matrix colMeans-methods: colMeans for snap objects colSums … WebbWrapper to run chromVAR on an assay with a motif object present. Will return a new Seurat assay with the motif activities (the deviations in chromatin accessibility across the set of … minigun script blood and iron