Youpu-Chen's repositories
Theta_D_H.Est
Calculator for statictics including Theta, D, H, and so on, based on the VCF input.
CPC-graph-based-NGS-pipeline
A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
deeplearning-biology
A list of deep learning implementations in biology
from-python-to-numpy
An open-access book on numpy vectorization techniques, Nicolas P. Rougier, 2017
FSTcalculator
For the calculation of FST
gene_lists
1) List of gene lists for genomic analyses. 2) for disease-related analysis
goatools
Python library to handle Gene Ontology (GO) terms
gwaslab
A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
hgv_modules
Teaching modules for Human Genome Variation Lab.
htslib
C library for high-throughput sequencing data formats
IntronPhaser
Python scripts that getting ortholog EPIC sequences for phylogenomic analysis.
jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
grideaBlog
Youpu's blog by Gridea
hpp_production_workflows
WDL’s and Dockerfiles for assembly QC process
ldsc
LD Score Regression (LDSC)
mergeVCF
to merge multiple VCF
mGSEA
modified gene set enrichment analysis (with a fuzzy ranked gene list)
PanGenome_VCF_PostProcess
A simple pipeline to process the VCF deconstructed from the VG pangenome graph
panGPT
A Transformer for Pangenome data
panpop
Application of pan-genome for population
popgen-notes
Population genetics notes
project-male-assembly
HGSVC SIG: targeted chromsome Y assembly
RainCloudPlots
Code and tutorials to visualise your data that is both beautiful *and* statistically valid
siyuan-themes-tsundoku-green
a simple and beautiful theme for siyuan-note
tutorials
Tutorials on phylogenetic and phylogenomic inference
WorldMapPlot
plot the world map using R
Youpu-Chen
Config files for my GitHub profile.
Zotero_configs
This repo is for Zotero configure files.