Sh1ne111

Shuai Chen's starred repositories

chep

Calculate Heterozygosity with Pileup

Language:Python600

eQTLseq

Hierarchical probabilistic models for multiple gene/variant associations based on NGS data

Language:Jupyter NotebookMIT500

pGWAS

pGWAS and functional filtering pipeline to identify candidate adaptive genetic traits in bacteria

Language:Perl1100

awesome-multitrait-gwas

List of software packages for multi-trait / multiple-trait / multivariate / high-dimensional GWAS

MIT2500

flye-kit

long reads assembly with Flye and Pilon

Language:PerlMIT400

A generic cross-platform C library that includes many commonly used components and frameworks, and a new scripting language interpreter. It currently supports C99 and Aspect-Oriented Programming (AOP).

Language:CBSD-3-Clause130400

polyploid-genotyping

SNP genotyping in polyploids

Language:C++NOASSERTION1500

vcf2sm

A fully automated pipeline for quantitative genotype calling from next generation sequencing data in polyploids

Language:PythonGPL-3.0100

eQTL_scripts

Set of scripts for eQTL, integrative biology work

Language:R700

eQTL

Language:PythonMIT400

TWAS

Example for TWAS

Language:RGPL-3.0700

twas

code to run twas utilizing https://github.com/gusevlab/fusion_twas to run the analysis

Language:Jupyter Notebook300

eGWAS

Language:Shell200

maffer

extract MSAs from genome variation graphs

Language:C++NOASSERTION3300

c2lib

A Perl/STL-like library of basics for C

Language:CNOASSERTION300

awesome-pangenomes

A list of software for pangenomics

MIT5900

appliedgenomics2022

Materials for EN.601.449/EN.601.649 Computational Genomics: Applied Comparative Genomics

Language:Jupyter NotebookCC0-1.02300

ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class.

Language:HTMLMIT16600

STC

A modern, user friendly, generic, type-safe and fast C99 container library: String, Vector, Sorted and Unordered Map and Set, Deque, Forward List, Smart Pointers, Bitset and Random numbers.

Language:CMIT125000

mlib

Library of generic and type safe containers in pure C language (C99 or C11) for a wide collection of container (comparable to the C++ STL).

Language:CBSD-2-Clause85100

qlibc

qLibc is a simple and yet powerful C library providing generic data structures and algorithms.

Language:CNOASSERTION95700

uthash

C macros for hash tables and more

Language:CNOASSERTION402800

course_Perl

天津医科大学，生物医学工程与技术学院，《Perl语言编程》课程资料

Language:HTML2200

jupyter-c-kernel

Minimal Jupyter C kernel

Language:PythonMIT57200

bcfanno

A fast and flexible program to annotate/interpret genetic variants in VCF/BCF file

Language:C1600

vcf2msa

convert a multi-sample VCF file to a multiple sequence alignment (C)

Language:C1300

TaFuCo

Targeted Fusion Caller (C)

Language:C300

MAC

Merging assemblies by using adjacency algebraic model and classification

Language:C++2200