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Proxy setting for R

Packages’ installation in R R packages are collections of functions and dataset developed by their authors. What are repositories? A repository is a plcae where packages are located so you can i...

Posted by Cooper on March 18, 2022

Usinng Mega 11 for phylogenetic tree analysis

Align 无奈我下的Mega11在 macOS Monterey下老是闪退，只好用commandline 运行Mega了。

Posted by Cooper on March 17, 2022

关于 Typora 的图片显示问题

在Typora中设置 Image 的路径：此后在Typora中插入图片后，图片的位置会自动保存在../img/md-post/${filename}，这里是指去上一个目录找img/md-post文件夹，${filename}是图片的文件名。而后，在写markdown的时候，将typora-root-url的路径设置为../,如下所示： 1 2 3 4 5 6 7 8 9 1...

Posted by Cooper on February 10, 2022

GenomicRanges Tutorial

#Introduction 1 2 3 4 if (!require("BiocManager")) install.packages("BiocManager") BiocManager::install("GenomicRanges") library(GenomicRanges) Reference: An Introduction to the GenomicRange...

Posted by Cooper on March 10, 2021

计算机网络基础

TCP/IP - 标准网络协议网络层次划分为了使不同计算机厂家生产的计算机能够相互通信，以便在更大的范围内建立计算机网络，国际标准化组织（ISO）在1978年提出了”开放系统互联参考模型”，即著名的OSI/RM模型（Open System Interconnection/Reference Model）。它将计算机网络体系结构的通信协议划分为七层，自下而上依次为：物理层（Phys...

Posted by Cooper on March 10, 2021

Configure Vim on Mac/Linux

Vim - the ubiquitous text editor Vim is a configurable text editor built to make creating and changing any kind of text very efficient. It is included as vi with most UNIX systems and with MacOS...

Posted by Cooper on March 2, 2021

Principle Component Analysis in R

参考画图目的：测试：筛选变异系数最大的前3个基因，对所有样本作PCA分析 1 2 3 4 5 6 7 8 9 10 11 12 library(useful) setwd("~/data/ciona_i/rna_seq/expression/stringtie/ref_only/") read.table("gene_ftkm_all_samples.tsv",header=TR...

Posted by Cooper on August 10, 2019

Sam 文件格式详解

sam文件介绍 SAM：The Sequence Alignment / Map format sam文件：两部分，sam header 和alignment section Some concepts linear alignment 1 An alignment of a read to a single reference sequence that may include ...

Posted by Cooper on March 1, 2019

Fasta 文件处理大全

# 1.文件格式介绍 3.统计查看有多少行： 1 grep '>' example.fasta | wc Fast 文件统计如果想对fastq文件进行统计，例如统计序列条数，碱基总数，reads读长分布等，可以使用seqkit工具进行操作： 1 seqkit stats 0_6_1.fq 0_6_2.fq 如果想统计fastq文件每条序列ATCG四种碱基组成以...

Posted by Cooper on February 20, 2019

Hisat tutorial

Hisat算法原理一、建立索引建立基因组索引 1 2 #NCBI: hisat2-build -p 4 GCF_000224145.3_KH_genomic (1).fna hisat2_index/ 建立基因组+转录组+SNP索引： bowtie2的索引只有基因组序列信息，tophat2比对时，转录组信息通过-G参数指定。HISAT2建立索引时，就应该把转录组信息加进...

Posted by Cooper on February 10, 2019