Pinned Repositories
3KRG-HAP
Haplotype marker based on 3,000 Rice Genomes for subpopulation inference
ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
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
ggomics
Visualization tools for genomics analysis based on ggplot2
PopGen
Small scripts for population genetics analysis
smartie-sv
calling SVs from Blasr contig level alignments
VCF2HAP
Construct gene haplotype with VCF format files and snpEff annotation.
VcfStat
Calculate and compare variation frequency and coverage in gatk vcf format files
zhuochenbioinfo's Repositories
zhuochenbioinfo/PopGen
Small scripts for population genetics analysis
zhuochenbioinfo/VCF2HAP
Construct gene haplotype with VCF format files and snpEff annotation.
zhuochenbioinfo/ABC-Enhancer-Gene-Prediction
Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
zhuochenbioinfo/ggomics
Visualization tools for genomics analysis based on ggplot2
zhuochenbioinfo/3KRG-HAP
Haplotype marker based on 3,000 Rice Genomes for subpopulation inference
zhuochenbioinfo/bioinformatics-one-liners
Bioinformatics one liners from Ming Tang
zhuochenbioinfo/CisDecoding_cistrome
zhuochenbioinfo/CisTransRegulation
Project description and analytic scripts for cis/trans regulation of fiber development in G. hirsutum
zhuochenbioinfo/epigenetics_scripts
Small scripts for epigenetics sequencing data analysis.
zhuochenbioinfo/gffread
GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
zhuochenbioinfo/giraffe-sv-paper
zhuochenbioinfo/hetPi
Nucleotide diversity estimation using VCF input with special treatment for heterozygous genotypes
zhuochenbioinfo/HFI
Haplotype Fixation Index for crop populations with homozygous nature, such as rice
zhuochenbioinfo/html_test
zhuochenbioinfo/KSNP-k-mer-based-haplotype-assembly
zhuochenbioinfo/MCScanX
MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
zhuochenbioinfo/minigraph
Proof-of-concept seq-to-graph mapper and graph generator
zhuochenbioinfo/NSR-nwad029
Codes used in NSR nwad029.
zhuochenbioinfo/pm4ngs
Project Manager for NGS data analysis
zhuochenbioinfo/PPanGGOLiN
Build a partitioned pangenome graph from microbial genomes
zhuochenbioinfo/psltools
Small tools to dissect BLAT psl format output.
zhuochenbioinfo/RiceENCODE-pipeline
zhuochenbioinfo/RiceReseqCNV
Mining CNV based on rice Nipponbare genome using resequencing data.
zhuochenbioinfo/riceTElib
A collection of manually curated TE examplars in rice (Oryza sativa).
zhuochenbioinfo/scLink
Inferring gene co-expression networks from single cell gene expression data
zhuochenbioinfo/simonhmartin-ABBA_BABA
Tutorials on evolutionary genomics
zhuochenbioinfo/TOP
zhuochenbioinfo/VcfWinSim
Calculate similarity between different samples using VCF format varaint data for IBS/IBD analysis.
zhuochenbioinfo/vg
tools for working with genome variation graphs
zhuochenbioinfo/zhuochenbioinfo.github.io