<?xml version="1.0" encoding="utf-8" ?><rss version="2.0"><channel><title><![CDATA[JjinYyi的博客]]></title><description><![CDATA[]]></description><link>https://blog.youkuaiyun.com/JjinYyi</link><language>zh-cn</language><generator>https://blog.youkuaiyun.com/</generator><copyright><![CDATA[Copyright &copy; JjinYyi]]></copyright><item><title><![CDATA[RNA-seq数据的GATK找变异流程]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/132564871</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/132564871</guid><author>JjinYyi</author><pubDate>Tue, 29 Aug 2023 17:30:56 +0800</pubDate><description><![CDATA[由于运行BAMixChecker软件需要构建过variant的bam文件，直接用RNA-seq STAR输出的bam文件会报字眼为“GATK  HaplotypeCaller…]]></description><category></category></item><item><title><![CDATA[WES|WGS]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/129665722</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/129665722</guid><author>JjinYyi</author><pubDate>Mon, 20 Mar 2023 13:36:00 +0800</pubDate><description><![CDATA[这个博主看下测试
wes生信技能树教程]]></description><category></category></item><item><title><![CDATA[RNA-seq fastp+STAR+featurecounts]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/129428045</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/129428045</guid><author>JjinYyi</author><pubDate>Fri, 10 Mar 2023 14:27:40 +0800</pubDate><description><![CDATA[STAR]]></description><category></category></item><item><title><![CDATA[linux RDKit | SMILES转MASCC或ECFP6]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/126867952</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/126867952</guid><author>JjinYyi</author><pubDate>Thu, 15 Sep 2022 11:34:37 +0800</pubDate><description><![CDATA[smiles转fingerprint]]></description><category></category></item><item><title><![CDATA[linux 下载pubchem文件]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/126479390</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/126479390</guid><author>JjinYyi</author><pubDate>Tue, 23 Aug 2022 10:17:27 +0800</pubDate><description><![CDATA[pubchem]]></description><category></category></item><item><title><![CDATA[R 免疫浸润CIBERSORT]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/125796774</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/125796774</guid><author>JjinYyi</author><pubDate>Fri, 15 Jul 2022 09:11:44 +0800</pubDate><description><![CDATA[免疫浸润CIBERSORT]]></description><category></category></item><item><title><![CDATA[Linux CentOS查看和修改PATH环境变量的方法]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/123002563</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/123002563</guid><author>JjinYyi</author><pubDate>Fri, 18 Feb 2022 14:24:41 +0800</pubDate><description><![CDATA[致敬大佬
查看PATH：echo $PATH
以添加mongodb server为列
修改方法一：
export PATH=/usr/local/mongodb/bin:$PATH

//配置完后可以通过echo $PATH查看配置结果。
生效方法：立即生效
有效期限：临时改变，只能在当前的终端窗口中有效，当前窗口关闭后就会恢复原有的path配置
用户局限：仅对当前用户
修改方法二：
通过修改.bashrc文件:
vim ~/.bashrc 

在最后一行添上：
export PATH=/usr/local]]></description><category></category></item><item><title><![CDATA[R venn图]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/121698962</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/121698962</guid><author>JjinYyi</author><pubDate>Fri, 03 Dec 2021 15:02:26 +0800</pubDate><description><![CDATA[常用
library(RColorBrewer)
color &lt;- brewer.pal(3, "Set3")

# Chart
venn.diagram(
        x = list(set1, set2, set3),
        category.names = c("Set 1" , "Set 2 " , "Set 3"),
        filename = 'venn2.png',
        output=TRUE,
        
        # 输出
     ]]></description><category></category></item><item><title><![CDATA[TCGA (linux下载)]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/121365199</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/121365199</guid><author>JjinYyi</author><pubDate>Wed, 17 Nov 2021 18:46:36 +0800</pubDate><description><![CDATA[1.gdc-client方法下载，含软件安装和下载命令
gdc-client download -m gdc_manifest_2021.txt -d ./
## -m的意思是下载manifest，后面接着文件列表的txt文件名称，-d是下载的文件药储存的地方

下载之后的文件，一个样本在一个文件夹下并且为gz格式

2.批量解压缩子目录中的gz文件：
 find . -name '*.gz' |xargs gunzip {}


3.整理合并所有样本的基因counts matrix
## R中运行
## ]]></description><category></category></item><item><title><![CDATA[linux (在linux运行R遇到的问题)]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/121131153</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/121131153</guid><author>JjinYyi</author><pubDate>Wed, 03 Nov 2021 21:43:34 +0800</pubDate><description><![CDATA[1.运行R显示"biobase"未安装
R语言安装并使用Biobase包:
install.packages("BiocInstaller", repos="https://bioconductor.org/packages/3.6/bioc")
BiocInstaller::biocLite("Biobase")

2.运行"library(NMF)“报错，提示运行"install.extras(NMF)”
直接运行"install.extras(NMF)"行不通，显示各种错误，例如
Error in c]]></description><category></category></item><item><title><![CDATA[R语言 NMF]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/120947853</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/120947853</guid><author>JjinYyi</author><pubDate>Mon, 25 Oct 2021 11:04:02 +0800</pubDate><description><![CDATA[R语言 NMF 如何自动判断最佳rank的数目
NMF层次聚类（较简单，可follow）
R语言实现非负矩阵分析（较详细，含原理）NMF包中包含不同的算法method,含对比代码

]]></description><category></category></item><item><title><![CDATA[limma包进行多组间差异表达]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/119785510</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/119785510</guid><author>JjinYyi</author><pubDate>Wed, 18 Aug 2021 17:53:41 +0800</pubDate><description><![CDATA[1.两组间阐述较清楚
2.大致相似，多组间差异表达看这里
3.生信技能树，含topTreat函数+韦恩图
4.生信星球，差异表达分子分母弄错了但解释较清楚

]]></description><category></category></item><item><title><![CDATA[各种聚类原理总结]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/116492737</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/116492737</guid><author>JjinYyi</author><pubDate>Fri, 07 May 2021 14:52:18 +0800</pubDate><description><![CDATA[MCL，马尔可夫聚类
如果你从一个点出发，到达其中的一个邻近点，那么你在簇内的可能性远大于离开当前簇而到达新簇的可能性——这就是MCL的核心思想。如果在一张图上进行多次的“Random Walks”，那么就有很大可能发现簇群，达到聚类的目的。而“Random Walks”的实现则是通过“Markov Chains”（马尔柯夫链）。

...]]></description><category></category></item><item><title><![CDATA[ChIP-seq 原理及实践]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/115859625</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/115859625</guid><author>JjinYyi</author><pubDate>Mon, 19 Apr 2021 10:57:21 +0800</pubDate><description><![CDATA[包含RNA-seq/ChIP-seq/ATAC-seq/scRNA-seq等原理及实践
这个可能更全面，之后仔细看吧
简书：有数据可以跟着做

]]></description><category></category></item><item><title><![CDATA[AUC]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/115332709</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/115332709</guid><author>JjinYyi</author><pubDate>Tue, 30 Mar 2021 18:44:38 +0800</pubDate><description><![CDATA[AUC，一文解疑

]]></description><category></category></item><item><title><![CDATA[Edge betweenness]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/115323416</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/115323416</guid><author>JjinYyi</author><pubDate>Tue, 30 Mar 2021 13:41:49 +0800</pubDate><description><![CDATA[只看开头的Edge betweenness解释即可

]]></description><category></category></item><item><title><![CDATA[R k.means及其聚类评估]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/115319978</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/115319978</guid><author>JjinYyi</author><pubDate>Tue, 30 Mar 2021 10:50:42 +0800</pubDate><description><![CDATA[1.k.means原理及实践
K-means介绍
使用R完成Kmeans聚类（不依赖包）
所需代码都有
2.聚类稳定性评估

]]></description><category></category></item><item><title><![CDATA[R语言 GO|KEGG]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/115082696</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/115082696</guid><author>JjinYyi</author><pubDate>Mon, 22 Mar 2021 16:13:44 +0800</pubDate><description><![CDATA[GO分析，参数写得详细
clusterProfiler，含代码‘
clusterProfiler: 分析+可视化GO和KEGG富集

]]></description><category></category></item><item><title><![CDATA[R 求具有重复行标签的值的和(for循环)]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/114935657</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/114935657</guid><author>JjinYyi</author><pubDate>Wed, 17 Mar 2021 16:19:04 +0800</pubDate><description><![CDATA[致敬原文章
library(plyr)
#示例表
a&lt;-data.frame("A"=c("a","b","a"),"B"=c(1,1,3),"C"=c(2,3,4))
#先求一列初始化
alldata&lt;-aggregate(C ~ A,data=a,sum)
#重命名避免重复
colnames(alldata)[2]&lt;-"test"
for (i in colnames(a)[2:length(colnames(a))]){
    #计算每列的和
    ter&lt;-aggrega]]></description><category></category></item><item><title><![CDATA[R 截断y轴]]></title><link>https://blog.youkuaiyun.com/JjinYyi/article/details/114599076</link><guid>https://blog.youkuaiyun.com/JjinYyi/article/details/114599076</guid><author>JjinYyi</author><pubDate>Tue, 09 Mar 2021 20:25:07 +0800</pubDate><description><![CDATA[提供了三种方法
这个更熟悉一点，基于ggplot2

]]></description><category></category></item></channel></rss>