zhuochenbioinfo

PopGen

Small scripts for population genetics analysis

VCF2HAP

Construct gene haplotype with VCF format files and snpEff annotation.

ABC-Enhancer-Gene-Prediction

Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)

ggomics

Visualization tools for genomics analysis based on ggplot2

3KRG-HAP

Haplotype marker based on 3,000 Rice Genomes for subpopulation inference

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

CisDecoding_cistrome

CisTransRegulation

Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum

gffread

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

giraffe-sv-paper

graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome

hetPi

Nucleotide diversity estimation using VCF input with special treatment for heterozygous genotypes

HFI

Haplotype Fixation Index for crop populations with homozygous nature, such as rice

html_test

KSNP-k-mer-based-haplotype-assembly

MCScanX

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

minigraph

Proof-of-concept seq-to-graph mapper and graph generator

NSR-nwad029

Codes used in NSR nwad029.

pm4ngs

Project Manager for NGS data analysis

PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes

psltools

Small tools to dissect BLAT psl format output.

RiceENCODE-pipeline

RiceReseqCNV

Mining CNV based on rice Nipponbare genome using resequencing data.

riceTElib

A collection of manually curated TE examplars in rice (Oryza sativa).

scLink

Inferring gene co-expression networks from single cell gene expression data

simonhmartin-ABBA_BABA

Tutorials on evolutionary genomics

TOP

VcfWinSim

Calculate similarity between different samples using VCF format varaint data for IBS/IBD analysis.

vg

tools for working with genome variation graphs

zhuochenbioinfo.github.io