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|man||2 years ago|
|BronchiCellPred.Rproj||2 years ago|
|DESCRIPTION||2 years ago|
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To predict bronchial cell proportions in bulk RNA-seq datasets
BronchiCellPred is an r package containing models for predicting the proportions of bronchial epithelial cells using bulk gene expression data from bronchial biopsies.
Gene signature matrix used for cell type deconvolution were generated using a single-cell RNAseq dataset of bronchial biopsies.
Three cell type deconvolution methods were available in this package, including nnls, MuSiC (https://github.com/xuranw/MuSiC) and BSeq-sc(https://github.com/shenorrLab/bseqsc). Users can choose the methods according to their own preference.
For additional details on methods and results please go our [manuscript](link to be updated).
library(devtools) install_github("CancanQi/BronchiCellPred") ## or install_github("CancanQi/BronchiCellPred",ref="HEAD")
Load the library and dependencies.
library(MuSiC) library(bseqsc) library(xbioc) library(reshape2) library(tidyverse) library(Biobase)
Prepare input data
## read bulk gene expression count table, with genes in row and samples in column count.table<-read.table("your file name") ## convert count table to expression set bulk.eset <- Biobase::ExpressionSet(assayData = data.matrix(count.table))
Predict bronchial cell proportions
## use the bulk expression set as the input, chose the methods from nnls, MuSiC and bseq est_prop<-BronCell.prop(bulk.eset,method="MuSiC") ## the output is a dataframe of cell proporion for each cell type (column) and each sample (row) ## plot the results BronCell.plot(est_prop)