Month: April 2021

TCseq可根据不同的聚类方法将基因按照表达模式分类 BiocManager::install(“TCseq”) library(TCseq) data <- read.delim(‘df_TCseq.xls’, row.names = 1, sep = ‘\t’, check.names = FALSE) data <- as.matrix(data) tca <- timeclust(data, algo = “cm”, k = 6, standardize = TRUE) #character string giving a clustering method. Options are km’ (kmeans), ‘pam’ (partitioning around medoids), ‘hc’ (hierachical clustering), ‘cm’ (cmeans). p <- timeclustplot(tca, value = “z-score(TPM)”,…

DNA甲基化：DNA甲基化为DNA化学修饰的一种形式，能在不改变DNA序列的前提下，改变遗传表现。为表观遗传编码的一部分，是一种外遗传机制。DNA甲基化过程会使甲基添加到DNA分子上，例如在胞嘧啶环的5’碳上：这种5’方向的DNA甲基化方式可见于所有脊椎动物。 在人类细胞内，大约有1%的DNA碱基受到了甲基化。 gzip -dc A.1_bismark_bt2_pe.deduplicated.CX_report.txt.gz > A.1_bismark_bt2_pe.deduplicated.CX_report.txt perl BismarkCX2methykit.pl A.1_bismark_bt2_pe.deduplicated.CX_report.txt #准备注释需要的bed文件（格式12） convert2bed -i gtf < out.gtf > out6.bed grep ‘exon’ out6.bed > aa && mv aa out6.bed python3 bed6Tobed12.py out6.bed > out12.bed#bed6Tobed12.py #methylKit安装及使用 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“methylKit”) library(methylKit) file.list = list(“A.CG_methykit.txt”,”B.CG_methykit.txt”,”C.CG_methykit.txt”,”D.CG_methykit.txt”,”E.CG_methykit.txt”,”F.CG_methykit.txt”,”G.CG_methykit.txt”,”H.CG_methykit.txt”,”I.CG_methykit.txt”) myobjDB=methRead(file.list, sample.id=list(“Control_1″,”Control_2″,”Control_3″,”Single_1″,”Single_2″,”Single_3″,”Multiple_1″,”Multiple_2″,”Multiple_3″), assembly=”HZGC”, treatment=c(0,0,0,1,1,1,2,2,2), context=”CpG”, mincov = 10, dbtype = “tabix”,…