Linhua-Sun

Ath_Heat_Hi-C

Bioinformatic analysis of RNA-Seq, WGBS, and Hi-C in Arabidopsis

faang-methylation

This repo is to collect the FAANG methylation group's code and pipelines

Q_lncRNA_analysis

TEanalysis

Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.

A_thaliana_epigenetic_mutants

bamTobw

Convert BAM files to bigWig files with a simple command

cLoops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

CLS_Sever_Code

FEELnc

FlExible Extraction of LncRNA

formattable

Formattable Data Structures

git_test

jbrowse

A modern genome browser built with JavaScript and HTML5.

Linhua-Sun.github.io

Webpage for Linhua Sun.

local_pca

Methods for examining PCA locally along the genome.

METACLUSTER

R package for context-specific functionality analysis of metabolic gene clusters

paratext

A library for reading text files over multiple cores.

PB

PB_CLS

Test on the phylogenomics of yeast

Population_Genetics

Start to Test Pop gen on BIG DATA

QIANLAB

SCRIPTS about analysis in QIANLAB

R-in-Centos-7

Use R!

resequecning_data_process

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

smcpp

SMC++ infers population history from whole-genome sequence data.

SVPV

Structural Variant Prediction Viewer

telescope

Quantification of transposable element expression using RNA-seq

test_circos

the-art-of-command-line

Master the command line, in one page

vcflib

a simple C++ library for parsing and manipulating VCF files, + many command-line utilities

ViewBS

ViewBS - Tools for exploring and visualizing bisulfite sequencing (BS-seq) data.