RNA profiling technologies at single-cell resolutions, including single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, scnRNA-seq for short), can help characterize the composition of tissues and reveal cells that influence key functions
cellannealallows the user to set four parameters. The first three govern the set of genes underlying the deconvolution process for each sample; the fourth parameter (iteration number) specifies for how long to run the optimisation process. Each parameter is discussed below. ...
Here, we asked if the high resolution nature of tissue-specific scRNA-Seq atlases can be leveraged to generate corresponding tissue-specific DNAm reference matrices, which, in conjunction with existing reference-based cell type deconvolution algorithms [6,14,18,19,20,21,22,23], would enable cell...
CellR: single-cell RNA-Seq guided deconvolution of cellular composition from bulk-tissue RNA-Seq - adoostparast/CellR
这个是出自于https://hbctraining.github.io/scRNA-seq/lessons/pseudobulk_DESeq2_scrnaseq.html 如下所示: 文末友情宣传 强烈建议你推荐给身边的博士后以及年轻生物学PI,多一点数据认知,让他们的科研上一个台阶: 生物信息学马拉松授课(买一得五),你的生物信息学入门课 ...
EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data Abstract Cell type heterogeneity presents a challenge to the interpretation of epigenome data, compounded by the difficulty in generating reliable single-cell DNA methylomes for large numbers of cells and ...
A pipeline to generate a Deep Neural Network cell type deconvolution model for bulk RNASeq samples from single cell rna-seq data. As described inTorroja and Sanchez-Cabo, 2019. Installation The pipeline runs in R 3.5.1 and python 3.6. ...
A library for the deconvolution of bulk cell samples using single-cell RNA expression data. - songlab-cal/rna-sieve
Therefore, deconvolution of bulk RNA-seq data with scRNA-seq atlas references can be a useful tool to help understand the TME. Keywords: liver cancer; tumour microenvironment; deconvolution 1. Introduction Liver cancer is one of the leading causes of cancer-related mortality worldwide, making up ...