Cran motifmatchr
WebDescribes spatial patterns of categorical raster data for any defined regular and irregular areas. Patterns are described quantitatively using built-in signatures based on co … WebchromVAR is an R package for the analysis of sparse chromatin accessibility. chromVAR takes as inputs aligned fragments (filtered for duplicates and low quality) from ATAC-seq or DNAse-seq experiments as well as genomic annotations such as motif positions. chromVAR computes for each annotation and each cell or sample a bias corrected ...
Cran motifmatchr
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WebMay 26, 2024 · The text was updated successfully, but these errors were encountered: WebMar 27, 2024 · In ( Hao*, Hao* et al, Cell 2024 ), we introduce ‘weighted-nearest neighbor’ (WNN) analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. This vignette introduces the WNN workflow for the analysis of multimodal single-cell datasets.
WebA rich hierarchy of matrix classes, including triangular, symmetric, and diagonal matrices, both dense and sparse and with pattern, logical and numeric entries. Numerous methods for and operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries. WebFind motif matches. matchMotifs (pwms, subject, ...) # S4 method for PWMatrixList,DNAStringSet matchMotifs (pwms, subject, genome = NULL, bg = c ("subject", "genome ...
WebThe package motifmatchr can be used to find motifs within peaks. The matchMotifs method takes as inputs the motif lists described above, or your own list of motifs, and returns a (Ranged)SummarizedExperiment with a matrix indicating what peaks (rows) contain what motifs (columns). library(BSgenome.Hsapiens.UCSC.hg19) WebWhile it is commonly accepted that structurally related TFs may have similar binding preference to sequences (i.e. motifs) and one TF may have multiple motifs, TF enrichment analysis is much more challenging than motif enrichment analysis. Here we present a R package for TF enrichment analysis which combine motif enrichment with the PECA model.
WebCRAN - Package ragg Anti-Grain Geometry (AGG) is a high-quality and high-performance 2D drawing library. The 'ragg' package provides a set of graphic devices based on AGG …
WebDescription. Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne … free heart screenings for womenWebTools for motif analysis in multi-level networks. Multi-level networks combine multiple networks in one, e.g. social-ecological networks. Motifs are small configurations of nodes … free heart screening ukWebOct 27, 2024 · motifmatchr: Fast Motif Matching in R Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, … blueberries southportWebContains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order. blueberries stock photoWebMethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along ... blue berries . straw berries cake mixWebmotifmatchr uses the MOODS C++ library (developedby Pasi Rastas, Janne Korhonen, and Petri Martinmaki) internally for motif matching. The primary method of motifmatchr … blueberries taste fishyWebNov 8, 2024 · w. parameter controlling size of window for filtration; default is 7. ranges. if subject is not GenomicRanges or RangedSummarizedExperiment, these ranges can be … blueberries supplements vs eating blueberries