chiongchih Goto Github PK

amplicon_datasets_for_drinking_water_microbiome

This is the repository for assessing 16S rRNA amplicon datasets from public repository such as NCBI, ERA...

anvio_command

Command and analysis workflow for anvio.

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

chiongchih.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

chiongchihgio_backup

clinker

Gene cluster comparison figure generator

cs-book

计算机类常用电子书整理，并且附带下载链接，包括Java，Python，Linux，Go，C，C++，数据结构与算法，人工智能，计算机基础，面试，设计模式，数据库，前端等书籍

dna-amino-acid-alignment

It's a python program which can align 2 DNA strands or amino acid strands.

ebola2014-phylodynamicspractical

Practical introduction to phylodynamics in R using Ebola sequence data

ense3142023

Metagenomic practical session for EnSE314 2023.

ense314_bioinformatics_results

This is the result of analysis

evolutionary-analysis-tool-of-single-amino-acid

This tool is coded by Changzhi Wang for Dr. Yue Chen’s lab in University of Minnesota, Twin City. And this tool based on database from PhosphositePlus (www.phosphosite.org/), Eggnog (http://eggnogdb.embl.de/#/app/home), WebGestalt (http://www.webgestalt.org/option.php) also including database from Uniprot (http://www.uniprot.org/).

faprotax_tutorial

This tutorial means to guide new users to do analysis based on FAPROTAX

fast-analyze-tool-of-homologous-expression-level-differences

Fast analyze tool of homologous expression level differences (FATHED) is a useful tool based on the famous tool Tophat by Johns Hopkins University( https://ccb.jhu.edu/software/tophat/index.shtml). And my new tool FATHED utilize the basic idea of tophat, while my attention is a higher efficiency and higher rate to analyze the large scale (human chromosomes level) datas and find out the special differences among different samples (same gene, different expression). FATHED can complete the job in a higher rate because it simplify the step of alignment. Each read will only be cut into 4 parts and align on genome randomly and once the disalign happened, FATHED will determine this read only depend on its alignment score (control by user). And the rpkm file will easily show the result of efficiency and score in a clear way.

gisaidr

Programmatically interact with the GISAID database.

ibex_command_line

iq-tree-treedater

kaustian_handbook_cn

KAUST生存手册

longread_tutorials

Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data

mazesolver

Find if a path exists in a maze for a rat trying to reach his piece of cheese

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metatranscriptome-workflow

Metatranscriptomics Tutorial

mobilegeneticelementdatabase

Contains a fasta format database of a large variety of mobile genetic elements and an annotation file

moving_to_ibex

my-academic-site

perfect-bacterial-genome-tutorial

planets

This is teaching repo for introduction to Git for Data Scientists

program-code-of-natural-gene-drift-prediction-nature-selection-factor-included-

It's a python program which utilize the random digit to predict the gene mutations during generations of specie. And this code include the nature selection factors.

program-code-of-standard-gene-drift-prediction

It's a python program which utilize the random digit to predict the gene mutations during generations of specie. And this code does not include the nature selection factors.

r-topics

R_Topics 内是WISE R Club历次专题课的课程资料