WebRecently, this R package has been extended to support chromatin data, e.g. ATAC. This extension package is called Signac. Seurat makes it possbile to integrate data from different technologies. Here, we will look at how Seurat and Signac can be used to integrate scATAC-seq and scRNA-seq data. WebchromVAR chromVAR: A package for computing variability across sets of peaks. Description Determine variation in chromatin accessibility across sets of annotations or …
Open science in scRNA-seq tools development. A GitHub summary...
WebMar 31, 2024 · The matrices obtained were further analyzed using Signac/Seurat (Hao et al., 2024), Chromvar (Schep et al., 2024) and Monocle (Cao et al., 2024; Trapnell et al., 2014). Contributor(s) Li R, Liu J, Yi P, Yang X, Hou S: Citation missing: Has this study been published? Please login to update or notify GEO. WebchromVAR is an R package for the analysis of sparse chromatin accessibility data from single cell or bulk ATAC or DNAse-seq data. The package aims to identify motifs or other … earl of strafford hooton roberts menu
Single-cell whole-genome amplification biases. Technical biases …
WebFeb 6, 2024 · Provides UI widget and layout functions for writing Shiny apps that work well on small screens. WebJan 1, 2024 · A BSgenome object or string stating the genome build recognized by getBSgenome. A peak x motif matrix. If NULL, pull the peak x motif matrix from a Motif object stored in the assay. Name of new assay used to store the chromVAR results. Default is … WebSep 26, 2024 · Chromatin Immunoprecipitation Sequencing (ChIP-seq) ( 12, 13) is a direct way to uncover TRs binding in the genome and determine their target genes at the bulk cell level. Compared to motifs, ChIP-seq is more accurate in defining cell-type-specific TR binding sites and investigating the genomic distribution for many non-DNA-binding CRs. earl of strafford hooton roberts