Pinned Repositories
3d-genome-processing-tutorial
A 3D genome data processing tutorial for ISMB/ECCB 2017
atac-seq-pipeline
ENCODE ATAC-seq pipeline
atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
awesome-R
A curated list of awesome R packages, frameworks and software.
ChrAccR
Analyzing chromatin accessibility data in R
chromVAR
chromatin Variability Across Regions (of the genome!)
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.
Microbial-Interkingdom-Suppl
Scripts and tables for Duran & Thiergart et al. 2018
ngsplot
Quick mining and visualization of NGS data by integrating genomic databases
Jessica-2019's Repositories
Jessica-2019/atac-seq-pipeline
ENCODE ATAC-seq pipeline
Jessica-2019/awesome-R
A curated list of awesome R packages, frameworks and software.
Jessica-2019/ChrAccR
Analyzing chromatin accessibility data in R
Jessica-2019/free-programming-books-zh_CN
:books: 免费的计算机编程类中文书籍，欢迎投稿
Jessica-2019/In-depth-NGS-Data-Analysis-Course
Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.
Jessica-2019/QTLseqr
QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
Jessica-2019/Zhang2019NBT
Scripts for stat and plot figures in rice microbiome paper
Jessica-2019/10x-scATAC-2019
Code Repository for Satpathy Granja et al 2019
Jessica-2019/awesome-single-cell
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Jessica-2019/Beautiful-Visualization-with-R
《R语言数据可视化之美》配套代码
Jessica-2019/bioawk
BWK awk modified for biological data
Jessica-2019/Burgess-Reyna_llorens-monocot-DNase
Scripts and analysis code for manuscript
Jessica-2019/Chorus2
A pipeline to select oligonucleotides for fluorescence in situ hybridization (Oligo-FISH).
Jessica-2019/deepTools
Tools to process and analyze deep sequencing data.
Jessica-2019/dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow
Jessica-2019/ggplot2
An implementation of the Grammar of Graphics in R
Jessica-2019/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.
Jessica-2019/HiC-Pro
HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
Jessica-2019/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Jessica-2019/jyanglab.github.io
Yang Lab @UNL website
Jessica-2019/lncRNA
De novo lncRNA discovery pipeline, re-write of PLAR by shell and awk
Jessica-2019/MSG-Book
:book: 现代统计图形 Modern Statistical Graphics
Jessica-2019/MutMap
MutMap pipeline to identify causative mutations responsible for a phenotype
Jessica-2019/Note
Jessica-2019/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.
Jessica-2019/QTL-seq
QTL-seq pipeline to identify causative mutations responsible for a phenotype
Jessica-2019/scMNase
Jessica-2019/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"
Jessica-2019/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."
Jessica-2019/Widespread-Long-range-Cis-Regulatory-Elements-in-the-Maize-Genome
scripts used for processing and analyzing data in the article.