YIGUIz's repositories
gtex_v9_data_analysis
Analyze GTEx (V9) Oxford Nanopore long-read RNA-Seq Transcript Quantification Data
processing-kit
Some self-written scripts used for pre-processing for graduate projects
scRNA-AHCA
Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
scSeq_convCOVID
Custom code for data analysis from "A single-cell atlas of lymphocyte adaptive immune repertoires and transcriptomes reveals age-related differences in convalescent COVID-19 patients"
bayesR
Bayesian hierarchical model for complex trait analysis
CamGWAS
Cameroon Malaria GWAS
Coursera-ML-AndrewNg-Notes
吴恩达老师的机器学习课程个人笔记
CrossMap
CrossMap is a python program to lift over genome coordinates from one genome version to another.
GMAT
Genomic Multivariate Analysis Tools
GWAS-pipline
the pipline of Genome-Wide Association Studies
NA12878
Data and analysis for NA12878 genome on nanopore
nadiv
R package that constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model').
Neuron
During brain development, neural stem cells (NSCs) undergo multiple fate-switches to generate various neuronal subtypes and glial cells, exhibiting distinct transcriptomic profiles at different stages. Despite the extensive transcriptomic characterization of human and mouse brain cells at bulk and single-cell levels, full-length transcriptomic data
ont_tutorial_transcriptome
A bioinformatics tutorial demonstrating the application of long read cDNA sequence data for the identification of differentially expressed genes and transcripts
Phragmites-australis-transcriptome-optimal-assembly
Workflow and scripts used for the assembly of the Phragmites australis transcriptome.
Plot
Just draw onec
python-animal-td-model
A BLUPF90 wrapper written in Python implementing the Animal Model, as well as Test-Day Model for estimating breeding values (EBVs)
PythonDemo
虾神的Python示例代码库
rd-imputation-accuracy
Phasing and genotype Imputation comparison. Have been evaluated: BEAGLE 5.2, EAGLE 2.4.1, SHAPEIT 4, MINIMAC 4, IMPUTE 5, using accuracy metrics like: IQS(Imputation Quality score), r2 (Pearson correlation), Concordance.
simtrait
Simulate Complex Traits from Genotypes
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
snp-pipeline
SNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
SNP_correlation_local_gEBV_variance
Rscript that conducts analysis of ‘corvar’, i.e., SNP correlation with variance of local gEBV
Soybean_salinity_ONT_DRS
Repo of scripts for analyzing soybean ONT DRS transcriptome under salt stress