Chiongchih
Bioinformatics; Computational biology; Multi-omics;
King Abdullah University of Science and TechnologyJeddah, Saudi Arabia
Pinned Repositories
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
DNA-amino-acid-alignment
It's a python program which can align 2 DNA strands or amino acid strands.
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/).
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.
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.
SUSTech-Course-Info
All the important parts of SUSTech Computer Science Courses
Very-Fast-Basic-Local-Alignment-Search-Tool-BLAST-
It's a python program which can be used for local alignment, which can be used to search a strand of DNA in whole human genome and find out in a very accurate position in less than 3 seconds(depends on server conditions).
Chiongchih's Repositories
Chiongchih/SUSTech-Course-Info
All the important parts of SUSTech Computer Science Courses
Chiongchih/Amplicon_datasets_for_drinking_water_microbiome
This is the repository for assessing 16S rRNA amplicon datasets from public repository such as NCBI, ERA...
Chiongchih/anvio_command
Command and analysis workflow for anvio.
Chiongchih/awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
Chiongchih/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/).
Chiongchih/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.
Chiongchih/Very-Fast-Basic-Local-Alignment-Search-Tool-BLAST-
It's a python program which can be used for local alignment, which can be used to search a strand of DNA in whole human genome and find out in a very accurate position in less than 3 seconds(depends on server conditions).
Chiongchih/chiongchih.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
Chiongchih/chiongchihgio_backup
Chiongchih/clinker
Gene cluster comparison figure generator
Chiongchih/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
Chiongchih/ebola2014-phylodynamicsPractical
Practical introduction to phylodynamics in R using Ebola sequence data
Chiongchih/EnSE3142023
Metagenomic practical session for EnSE314 2023.
Chiongchih/EnSE314_bioinformatics_results
This is the result of analysis
Chiongchih/FAPROTAX_tutorial
This tutorial means to guide new users to do analysis based on FAPROTAX
Chiongchih/GISAIDR
Programmatically interact with the GISAID database.
Chiongchih/ibex_command_line
Chiongchih/IQ-tree-Treedater
Chiongchih/KAUSTian_Handbook_CN
KAUST生存手册
Chiongchih/LongRead_tutorials
Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
Chiongchih/Metagenome-assembled-genomes-pipeline
Up to date MAG pipeline
Chiongchih/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Chiongchih/Metatranscriptome-Workflow
Metatranscriptomics Tutorial
Chiongchih/MobileGeneticElementDatabase
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
Chiongchih/Moving_to_IBEX
Chiongchih/my-academic-site
Chiongchih/Perfect-bacterial-genome-tutorial
Chiongchih/planets
This is teaching repo for introduction to Git for Data Scientists
Chiongchih/sarscov2Rutils
Chiongchih/Statistical-suggestion-for-amateur
This repository is noted for amateurs of statistics who is looking for suggestion in their analysis.