58 lines
1.9 KiB
Markdown
58 lines
1.9 KiB
Markdown
# BronchiCellPred
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To predict bronchial cell proportions in bulk RNA-seq datasets <br>
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https://github.com/CancanQi/BronchiCellPred/
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![introduction](https://github.com/CancanQi/BronchiCellPred/blob/ca0893d545d6adcac28c81b3ff6fd9d911f31ef4/introduction.png)
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## Introduction
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`BronchiCellPred` is an r package containing models for predicting the proportions of bronchial epithelial cells using bulk gene expression data from bronchial biopsies. <br>
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Gene signature matrix used for cell type deconvolution were generated using a single-cell RNAseq dataset of bronchial biopsies.<br>
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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. <br>
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For additional details on methods and results please go our [manuscript](link to be updated).
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## Installation
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```R
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library(devtools)
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install_github("CancanQi/BronchiCellPred")
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## or
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install_github("CancanQi/BronchiCellPred",ref="HEAD")
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```
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## Quick start
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#### Load the library and dependencies.
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```R
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library(MuSiC)
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library(bseqsc)
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library(xbioc)
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library(reshape2)
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library(tidyverse)
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library(Biobase)
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```
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#### Prepare input data
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```R
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## read bulk gene expression count table, with genes in row and samples in column
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count.table<-read.table("your file name")
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## convert count table to expression set
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bulk.eset <- Biobase::ExpressionSet(assayData = data.matrix(count.table))
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```
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#### Predict bronchial cell proportions
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```R
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## use the bulk expression set as the input, chose the methods from nnls, MuSiC and bseq
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est_prop<-BronCell.prop(bulk.eset,method="MuSiC")
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## the output is a dataframe of cell proporion for each cell type (column) and each sample (row)
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## plot the results
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BronCell.plot(est_prop)
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```
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![result](https://github.com/CancanQi/BronchiCellPred/blob/ca0893d545d6adcac28c81b3ff6fd9d911f31ef4/main_result.png)
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