Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data - dylkot/cNMF
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5Branches0Tags Code This branch is117 commits behinddylkot/cNMF:main. README MIT license cNMF is an analysis pipeline for inferring gene expression programs from single-cell RNA-Seq (scRNA-Seq) data. It takes a count matrix (N cells X G genes) as input and produces a (K x G) matrix...
Constrained Nonnegative Matrix Factorization for microEndoscopic data. 'E' also suggests 'extension'. It is built on top ofCNMFwith supports to 1 photon data. Download OPTION 1: download the package using thisLINK OPTION 2: (recommended) clone the git repositoryhttps://github.com/zhoupc/CNMF_...
另外,将功能基因集合进行富集分析(如GO和GEVA)可以更好地解读基因功能集合所对应的功能,对后期寻找疾病相关的标志基因提供更多的可能性。 参考:https://github.com/dylkot/cNMF/blob/master/Tutorials/analyze_simulated_example_data.ipynb https://github.com/dylkot/cNMF/tree/master?tab=readme-ov-file...
Download OPTION 1: download the package using thisLINK OPTION 2: (recommended) clone the git repositoryhttps://github.com/zhoupc/CNMF_E.git. In this way, you are able to get the latest updates of the package within 1-line command or 1-button click. ...
github上的图挺形象的,从左到右把细胞信息转化成基因矩阵然后进行分解提取。 步骤流程 R语言部分 1、导入 rm(list=ls()) options(stringsAsFactors = F) library(Seurat) library(ggplot2) library(qs) library(BiocParallel) register(MulticoreParam(workers = 4, progressbar = TRUE)) ...
github上的图挺形象的,从左到右把细胞信息转化成基因矩阵然后进行分解提取。 步骤流程 R语言部分 1、导入 代码语言:javascript 代码运行次数:0 运行 AI代码解释 rm(list=ls())options(stringsAsFactors=F)library(Seurat)library(ggplot2)library(qs)library(BiocParallel)register(MulticoreParam(workers=4,progressbar...
Hey there--thanks for developing this! Really excited to explore it, but I keep hitting an error during k_selection_plot I exported a count matrix (1775 cells in rows, genes in columns) from Seurat (only cells/genes with sum != 0) as a t...
Code Issues14 Pull requests Actions Projects Security Insights Additional navigation options main 7Branches0Tags Code Folders and files Name Last commit message Last commit date Latest commit dylkot Merge branch 'development' into 'master' Mar 2, 2025 ...