yirenheihei's repositories
snakepipes
A toolkit based on snakemake and python for analysis of NGS data
atac-seq-pipeline
ENCODE ATAC-seq pipeline
atacseq-1
ATAC-seq peak-calling, QC and differential analysis pipeline.
awesome-deep-learning-papers
The most cited deep learning papers
bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
ChIP-seq-analysis
ChIP-seq analysis notes from Ming Tang
ChIP-seq_tutorial
ChIP-Seq Analysis Tutorial
chipseq_pipeline
AQUAS TF and histone ChIP-seq pipeline
Chloroplast-genome-assembly
A pipeline for assemble chroloplast genome using short/long reads
CONCOCT
Clustering cONtigs with COverage and ComposiTion
CS-Books
📚 Computer Science Books 计算机技术类书籍 PDF
DeepLearning
Python for《Deep Learning》，该书为《深度学习》(花书) 数学推导、原理剖析与源码级别代码实现
DeepNude-an-Image-to-Image-technology
DeepNude's algorithm and general image generation theory and practice research, including pix2pix, CycleGAN, UGATIT, DCGAN, and VAE models (TensorFlow2 implementation). DeepNude的算法以及通用GAN图像生成的理论与实践研究。
fasta_GCN
使用图卷积对生物序列进行分类
Fijarczyk2020_JeanTalon
Custom code for the paper about the Jean-Talon beer strain
GWA_tutorial
A comprehensive tutorial about GWAS and PRS
HTseq_2019
workshop content for HTseq 2019
HUPAN
Human pan-genome analysis pipeline
pan-genome-analysis
Processing pipeline for pan-genome visulization and exploration
PhaME
Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.
pilon
Pilon is an automated genome assembly improvement and variant detection tool
protein-vae
Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies
rnaseq
RNA sequencing analysis pipeline using STAR, HISAT2 and Salmon with gene counts and quality control
SingleR
SingleR: Single-cell RNA-seq cell types Recognition
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.
snvphyl-tools
Tools/scripts for the SNVPhyl whole genome phylogenomics pipeline
variant-calling-pipeline-gatk4
Variant Calling Pipeline Using GATK4 and Nextflow
wsi-preprocessing
Simple library for preprocessing histopathological whole-slide images (WSI) into tiles (a.k.a. patches) towards deep learning