第一步 获取染色体长短臂位置注释 http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/ wget http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz gunzip cytoBand.txt.gz 1234567891011121314151617

第一步 获取对应物种的基因位置注释文件 https://www.gencodegenes.org/human/ wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode\_human/release\_39/gencode.v39.chr\_patch\_hapl\_scaff.annotation.gtf.gz gunzip gencode

conda create -n rinferCNV -c conda-forge r-base=4.1.2 -y conda activate rinferCNV conda install -c conda-forge r-seurat=4.1.0 -y conda install -c conda-forge r-irkernel=1.3 -y conda in

conda create -n rcBioPortal -c conda-forge r-base=4.1.2 -y conda activate rcBioPortal conda install -c conda-forge r-cgdsr=1.3.0 -y conda install -c conda-forge r-irkernel=1.3 -y R IRk

定义一些辅助函数1234library(ggsci)f_levels2col <- function(df_f, col){ col[as.numeric(df_f)]} 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051f_ge

定义绘图函数12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667686970717273747576777879808182838485868788899091929394959697989910010

火山图 https://mp.weixin.qq.com/s/TvAor9voh\_kDnIxsC-U48w https://www.bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html 12345678library(EnhancedVolcano)data

conda install -c conda-forge r-openxlsx=4.2.5 -y 1openxlsx::read.xlsx(xlsxFile = "marker.xlsx", sheet = 1, colNames = F)

conda create -n rplot -c conda-forge r-base=4.1.2 -y conda activate rplot conda install -c conda-forge r-seurat=4.1.0 -y conda install -c conda-forge r-irkernel=1.3 -y R IRkernel::inst

第一步 下载自带的参考数据库（仅需一次，已经运行过了，跳过）123456789library(celldex)ref_HPCD <- HumanPrimaryCellAtlasData() ref_BFD <- BlueprintEncodeData() ref_MRD <- MouseRNAseqData() ref_IGD <- ImmGenData() ref_DIC