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README.md

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 # BronchiCellPred
+To predict bronchial cell proportions in bulk RNA-seq datasets
+
+![introduction](https://github.com/CancanQi/BronchiCellPred/blob/ca0893d545d6adcac28c81b3ff6fd9d911f31ef4/introduction.png)
+
+## Introduction
+
+`BronchiCellPred` is an r package containing models for predicting the proportions of bronchial epithelial cells using bulk gene expression data from bronchial biopsies. <br>
+Gene signature matrix used for cell type deconvolution were generated using a single-cell RNAseq dataset of bronchial biopsies.<br>
+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>
+For additional details on methods and results please go our [manuscript](link to be updated).
+
+## Installation
+
+library(devtools)
+install_github("xxx/BronchiCellPred")  (to be updated)
+
+## Quick start
+
+#### Load the library and dependencies.
+
+```R
+library(MuSiC)
+library(bseqsc)
+library(xbioc)
+library(reshape2)
+library(tidyverse)
+library(Biobase)
+```
+
+#### Prepare input data
+
+```R
+## 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
+
+```R
+## 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)
+
+```
+![result](https://github.com/CancanQi/BronchiCellPred/blob/ca0893d545d6adcac28c81b3ff6fd9d911f31ef4/main_result.png)
+
+