Zhaoxu-Gao's repositories
higlass
Fast, flexible and extensible genome browser.
cooltools
The tools for your .cool's
pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
cooler
A cool place to store your Hi-C
HiC_tools
A collection of tools for Hi-C data analysis
the-art-of-command-line
Master the command line, in one page
pareidolia
Multi-sample change detection in Hi-C patterns
smcpp
SMC++ infers population history from whole-genome sequence data.
GENOVA
GENome Organisation Visual Analytics
fanc
FAN-C: Framework for the ANalysis of C-like data
fithic
Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
hicreppy
Python reimplementation of hicrep with compatibility for sparse matrices
CoolBox
Jupyter notebook based genomic data visualization toolkit.
chromosight
Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps
telescope
Quantification of transposable element expression using RNA-seq
iCount
iCount, protein-RNA interaction analytics
HiCorr
HiCorr: a Hi-C data bias-correction pipeline
ViewBS
ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GeneNeighborhood
Analyze the neighborhood (upstream/downstream neighbors) of any gene set
MotifSearcher
Here, we describe and provide an RNA-Seq analysis of a RIP assay to understand the mechanism of AML del(9q) progression.
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.
FEELnc
FEELnc : FlExible Extraction of LncRNA
METACLUSTER
R package for context-specific functionality analysis of metabolic gene clusters
RIPSeq-Listeria
RIP-Seq and RNA-Seq of an RNA-binding protein secreted by Listeria monocytogenes which activates RIG-I signaling Secreted bacterial
HiCAssembler
Software to assemble contigs/scaffolds into chromosomes using Hi-C data
Widespread-Long-range-Cis-Regulatory-Elements-in-the-Maize-Genome
scripts used for processing and analyzing data in the article.
TEanalysis
Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.
iHiC
A set of C++ utilities for data pre/post-procession to faciliate Hi-C data analysis with public software