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原创 为window配置相关的生信环境
安装Ubuntu子系统安装zsh环境在Ubuntu子系统中安装conda安装jupyter notebook在windows中安装R和Rstudio
2023-12-30 11:20:38
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原创 Sed and Awk 101 Hacks --2 AWK学习
Sed and Awk 101 Hacks <2> AWK学习Chr8、awk语法和脚本命令awk 命令语法awk -Fs '/pattern/ {action}' input-file (or)awk -Fs '{action}' intput-file$ awk -F: '/mail/ {print $1}' /etc/passwd mail awk -Fs -f myscript.awk input-fileawk 程序结构(BEGIN,body,END
2022-05-06 11:54:46
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原创 Sed and Awk 101 Hacks --1-sed 命令学习
Sed and Awk 101 Hacks(Chr1: sed syntax and basic commands)1.sed command syntax$ cat >employee.txt101,John Doe,CEO102,Jason Smith,IT Manager103,Raj Reddy,Sysadmin104,Anand Ram,Developer105,Jane Miller,Sales Manager2.print (P)#仅打印第二行$ sed -n '
2022-05-05 15:33:55
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原创 Notes of Python Cookbook (Chr4-Chr6)
第四章:迭代器与生成器4.1 手动遍历迭代器遍历一个可迭代对象中的所有元素,但是却不想使用 for 循环。使用 next() 函数并在代码中捕获 StopIteration 异常。比如,下面的例子手动读取一个文件中的所有行# def manual_iter():# with open('/etc/passwd') as f:# try:# while True:# line = next(f)#
2022-04-14 16:07:48
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原创 Notes of Python Cookbook (Chr1-Chr3)
贴子主要关于自己的读书摘要,涉及到侵权请联系删除第一章:数据结构和算法# 任何的序列(或者是可迭代对象)可以通过一个简单的赋值语句解压并赋值给多# 个变量。唯一的前提就是变量的数量必须跟序列元素的数量是一样的。p= (4,5)x,y = pprint(x,y,end='\n')# 1.2 解压可迭代对象赋值给多个变量record = ('Dave', 'dave@example.com', '773-555-1212', '847-555-1212')name, email, *phon
2022-04-13 20:43:47
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原创 利用BioEdit软件进行短序列序列比对之查看突变位点
该教程主要适用于基因突变后查看突变位点下载安装包:http://www.mbio.ncsu.edu/bioedit/page2.html,这个站点直接点击Download BioEdit.zip (Full install: ca. 11.9 Mb)下载即可已知得出:敲除基因的Sanger sequencing 结果1、直接打开xx.ab1 文件直接跳出如下界面(软件已安装的条件下)2、导入参考序列点击sequence,选new sequnce3、出现如下界面,在红色框框中输入备注,并选
2022-01-06 15:06:19
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原创 Linux&Ubuntu安装zsh环境
Ubuntu子系统都是一样的安装本教程只配置简易的zsh:oh-my-zshsh -c "$(curl -fsSL https://raw.github.com/robbyrussell/oh-my-zsh/master/tools/install.sh)"主题方面:个人比较喜欢:ys更多主题参考
2021-12-23 15:48:53
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原创 01_Dive_into_python (reading note)
难度:*Don’t bury your burden in saintly silence. You have a problem?page 41如有涉及到**知识版权,联系删除SUFFIXES = {1000: ['KB', 'MB', 'GB', 'TB', 'PB', 'EB','ZB', 'YB'], 1024: ['KiB', 'MiB', 'GiB', 'TiB', 'PiB','EiB', 'ZiB', 'YiB']}def approximate_siz
2021-11-30 20:52:16
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原创 R和pands 实现dataframe的Z-score
1、导入函数from scipy.stats import zscore2、实现按行或列的z分数df4=pd.DataFrame(zscore(df3,axis=1)) #实现每行的数据的z分数df4=pd.DataFrame(zscore(df3,axis=0)) #实现每列的数据的z分数sample:实现每行的z分数......
2021-08-02 16:36:49
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原创 rice kegg enrichment
setwd('D:\\11_NM_DNAmeth\\02_DMs_DMR_gene\\04_new_DMR_DEG_GO\\rapid/')library('clusterProfiler')library(topGO)library(AnnotationHub)library(dbplyr)library(ggplot2)library(pathview)hub <- AnnotationHub() query(hub, 'Oryza sativa')rice <- h
2021-05-28 09:10:27
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原创 关于R包安装及python包的安装(持续更新)
本文主要介绍MAnorm2及MAnorm2_utils的安装1、关于R包的下载及手动安装下载好安装包gz文件install.packages("/path/to/the/package.gz", repos = NULL)2、关于python包的下载及安装下载好安装包gz文件先解压,然后一般会有setup.py文件python ./setup.py installpython -c 'import MAnorm2_utils'相关链接:github...
2021-04-23 10:00:51
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原创 关于ubuntu子系统ip和远程登录问题及移动硬盘的挂载
1.移动硬盘的挂载## 移动硬盘的挂载sudo mkdir /mnt/Hsudo mount -t drvfs H:\ /mnt/H## 卸载sudo umount /mnt/e## 必须卸载,这样才能正常弹出,否则会提示一直占用。## 下次用的话还需重新挂载2.远程登录问题如果以下命令没输出结果,则需要安装ssh服务ps -e | grep ssh安装命令sudo apt-get install openssh-server 然后再启动服务/etc/init.d/ssh
2021-04-21 11:02:19
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原创 黑白bar_sd_并添加text
setwd('D:\\11_NM_DNAmeth\\01_数据情况')library(reshape2)library(ggpubr)library(readxl)df1<-read_excel('1_甲基化占比.xlsx')head(df1)data<-df1unique(data$sample)aa<-round(data$percentage,4)data$label=paste(aa*100, "%", sep='')# data$sample<- fac
2021-04-20 16:46:59
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原创 boxplot_pair_显著性
setwd('D:\\11_NM_DNAmeth\\06_all_meth/')library(ggplot2)library(ggsignif)library(ggpubr)data<-read.table('./4_twobed_sin.txt',header = 0)head(data)colnames(data)<-c('sample2','level','type','value')#'sample',table(data$sample2)table(data$type
2021-04-09 17:28:58
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原创 DMR_DMS_ggline
setwd('D:\\11_NM_DNAmeth\\02_DMs_DMR\\02_DMS')library(ggplot2)data1<-read.table('./1plot_density.txt',header = 0)[3:4]# colnames(data1)<-c('context','value')colnames(data1)<-c('context','value')head(data1)> head(data1) context value1
2021-04-08 21:13:06
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原创 DMR_DMS_bar
setwd('D:\\11_NM_DNAmeth\\02_DMs_DMR\\02_DMS')library(ggplot2)data1<-read.table('./1plot_density.txt',header = 0)[3:4]# colnames(data1)<-c('context','value')colnames(data1)<-c('context','value')head(data1)> head(data1) context value1
2021-04-08 21:05:46
153
原创 GO term heatmap and dot pic
setwd('D:\\11_NM_DNAmeth\\02_DMs_DMR\\02_DEG_DMR')data3<-read.table('go.txt',sep='\t',header = 1)# colnames(data)<-c('T_specific',)library(ggplot2)library(dplyr)library(reshape2)colnames(data3)data<- melt(data3,id.vars=c("Description","Onto
2021-03-17 21:58:04
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原创 分面boxplot
setwd('D:\\11_NM_DNAmeth\\02_DMs_DMR\\01_hyper_hypo')library(ggplot2)library(ggsignif)library(ggpubr)data<-read.table('./DMR_hyp_methLevel.txt',header = 0)colnames(data)<-c('sample','sample2','level','type','value')table(data$sample2)table(da
2021-03-17 19:37:13
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原创 横向堆积柱状图(peak distribution)
横向堆积柱状图,并添加标签setwd('D:\\12_G4NaK_PEG\\04_PQS\\01_anno')data<-read.table('1G2VSG3.txt')library(reshape2)library(ggpubr)colnames(data)<-c('Sample','type','feature','number','all','baifen')data$feature<- factor(data$feature,
2021-03-16 18:50:11
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原创 cirque圆环图(g4)
setwd('D:\\12_G4NaK_PEG\\04_PQS')library(ggplot2)library(ggpubr)data<-read.table('1plot_pie.txt')colnames(data)<-c("value","number","sample","type")data$value<-round(data$value,4)data$lab<-paste0(data$value*100, "%")df1=data[1:5,]table
2021-03-16 15:52:58
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原创 bar plot and sort plot by the size of the value
setwd('D:\\12_G4NaK_PEG\\04_PQS')library(readxl)library(reshape2)library(ggplot2)number<-read.table('1number.txt',header = 1)colnames(number)data<-melt(number,id.vars="sample",variable.name="Type", value.name="value")library(stringr
2021-03-16 09:51:56
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原创 boxplot_mul_sig
setwd('D:\\12_G4NaK_PEG\\03_seq_trait')data<-read.table('1peak_GCcontent.txt')colnames(data)<-c('model','value')library(reshape2)library(ggpubr)library(ggsignif)head(data)> head(data) model value1 Common 0.62032092 Common 0.6273585
2021-03-15 17:13:36
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原创 GCcontent-boxplot
setwd('D:\\12_G4NaK_PEG\\03_seq_trait')data<-read.table('1peak_GCcontent.txt')colnames(data)<-c('model','value')library(reshape2)library(ggpubr)library(ggsignif)head(data)> head(data) model value1 Common 0.62032092 Common 0.6273585
2021-03-15 16:38:42
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原创 绘制曲线ggline
setwd('D:\\12_G4NaK_PEG\\03_seq_trait')data<-read.table('1plot_allskew.txt')library(reshape2)library(ggpubr)colnames(data)<-c("region",'sample','v1','v2',"type")# data$sample<- factor(data$sample,# levels= c('Common','PQ
2021-03-15 16:11:01
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