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songlov3 (cxsong)

cxsong

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vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Language:PythonLicense:GPL-3.0Stargazers:276Issues:0Issues:0

LDkit

LDkit: a parallel computing toolkit for linkage disequilibrium analysis

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warpedLMM

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KEGG_extractor

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Dynamic-chromatin-regulatory-programs-during-embryogenesis-of-hexaploid-wheat

code for the publication "Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat"

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hap-ibd

The hap-ibd program detects identity-by-descent segments in phased genotype data.

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vcf_to_qtl

R script for conversion of vcf file to r/qtl format for subsequent getetic map construction

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Foxtail-millet-data-analysis

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ggtraces

A tidyverse and grammar of graphics powered line traces visualizer

License:MITStargazers:26Issues:0Issues:0

SimpleTidy_GeneCoEx

A simple gene co-expression analyses workflow powered by tidyverse and graph analyses

License:MITStargazers:172Issues:0Issues:0

scripts

Scripts for analysis used during the course

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SAP_WGS

Whole-genome sequencing of the Sorghum Asssociation Panel

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ldblock

Plot LD blocks around an association peak

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Population_RNA-seq

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mapping_scripts

This github repository contains the original code from the article “Genetic mapping of host loci influencing gut microbiome composition in hybrid mice” published in …

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MutFinder

A pipeline to identify causal mutations in EMS mutant

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DIVERSE_MAGIC_WHEAT

16-parent wheat MAGIC population

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LDdecay

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PopLDdecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

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QTLseqr

QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis

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PopGen

Small scripts for population genetics analysis

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XPCLR

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GWA_tutorial

A comprehensive tutorial about GWAS and PRS

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Population_Genetics_in_R

A primer for computational tools to analyze genetics of populations in R

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Work_flow_of_population_genetics

整理常用的群体遗传学分析流程和脚本

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genomics_general

General tools for genomic analyses.

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owwc

repository for code used in analysis of open wild wheat consortium

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maize_eQTL

a set of data and scripts to perform eQTL mapping in MAGIC RILs

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bio_tools

Useful bioinformatic scripts

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my_script

my commonly used perl script

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