Yingshan Li

TRUTH, BEAUTY, KINDNESS

Bioinformatics

Reusable Perl scripts in bioinformatics analysis

1. Submit jobs to server #!/bin/sh #PBS -N NEG_AUP_velvet #PBS -j oe #PBS -q BIG cd /home/yli/data/fwater_virome/Negative 2. If a file presents, then delete if (-e "APL_RNA_contig_ORFs.txt")...

Posted by Yingshan Li on December 8, 2020

Introduction to Perl

Introduction of the basic data structures and grammars in Perl

Data structure Scalar Creation: $age = 25; # numeric $name = "runoob"; # string $string = 'This is a multiline string'; #multiline string Operations: Context is everywhere...

Posted by Yingshan Li on November 8, 2020

Handling files and errors in Python

Handling files and errors in Python

File IN/OUT The era of genomics has produced a sea of sequencing data. The first thing a bioinformatician needs to do is to read the data into the program. When the analysis is done, the results pr...

Posted by Yingshan Li on October 8, 2020

Object-oriented programming in Python

Introduction to object-oriented programming in Python, including packaging, inheritence, and porlimorphism

Object-oriented programming (OOP) Procedural programming is about writing procedures or functions that perform operations on the data, while object-oriented programming is about creating objects t...

Posted by Yingshan Li on September 8, 2020

Functions and packages in Python

Introduction to creat and use functions and packages in Python

Basics of function Define and call functions Define function：There are many build-in functions in Python such as print(). However, you can also define your own functions. The basic format to defi...

Posted by Yingshan Li on August 8, 2020

Basic grammers in Python

Introduction to data structures, types of variables, condition control, loop structrue etc.

Preface Hello everyone! My name is Yingshan Li. This is a basic tutorial for greeners to start Python programming. Python is one of the most elegant and simple programming languages with incredibl...

Posted by Yingshan Li on July 8, 2020

Introduction to Linux-shell

Introduction to Shell scripting

Introduction A shell script is a computer program designed to be run by the Unix shell, a command-line interpreter. The various dialects of shell scripts are considered to be scripting languages. ...

Posted by Yingshan Li on June 8, 2020

Introduction to Vim

Introduction to how to efficiently use Vim in Linux and Unix environment

Brief introduction Vim is a highly configurable text editor built to enable efficient text editing. It is an improved version of the vi editor distributed with most UNIX systems. Vim is often call...

Posted by Yingshan Li on May 8, 2020

Linux command lines

Introduction to the most commonly used command lines in Linux and Unix environment

The command line (also called the console or terminal) is a text-based interface within the operating system, that forwards commands from the user to the operating system. This makes it possible, f...

Posted by Yingshan Li on April 8, 2020

R programming-Graphics

Introduction to generating graphics in R

Parameters in R plotting (function par() is used to define parameters in R plotting) Choose the righ “type” in R plotting type= ”p “ Plot points in graphics type= ”l “  Plot lines in graphic...

Posted by Yingshan Li on March 8, 2020

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