Zhanjie Li's repositories
atac-seq-pipeline
ENCODE ATAC-seq pipeline
free-programming-books-zh_CN
:books: 免费的计算机编程类中文书籍，欢迎投稿
In-depth-NGS-Data-Analysis-Course
Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.
Zhang2019NBT
Scripts for stat and plot figures in rice microbiome paper
10x-scATAC-2019
Code Repository for Satpathy Granja et al 2019
awesome-single-cell
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Beautiful-Visualization-with-R
《R语言数据可视化之美》配套代码
bioawk
BWK awk modified for biological data
Burgess-Reyna_llorens-monocot-DNase
Scripts and analysis code for manuscript
Chorus2
A pipeline to select oligonucleotides for fluorescence in situ hybridization (Oligo-FISH).
deepTools
Tools to process and analyze deep sequencing data.
dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
ggplot2
An implementation of the Grammar of Graphics in R
gimmemotifs
Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.
HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
jyanglab.github.io
Yang Lab @UNL website
lncRNA
De novo lncRNA discovery pipeline, re-write of PLAR by shell and awk
MSG-Book
:book: 现代统计图形 Modern Statistical Graphics
MutMap
MutMap pipeline to identify causative mutations responsible for a phenotype
phantompeakqualtools
This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
QTL-seq
QTL-seq pipeline to identify causative mutations responsible for a phenotype
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"
The-prevalence-evolution-and-chromatin-signatures-of-plant-regulatory-elements
Scripts used for processing and analyzing data in the article "The prevalence, evolution and chromatin signatures of plant regulatory elements."
Widespread-Long-range-Cis-Regulatory-Elements-in-the-Maize-Genome
scripts used for processing and analyzing data in the article.