mengmeng-jiang / TDGP Public

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my 3D genome pipeline and scripts repository

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Name		Name	Last commit message	Last commit date
Latest commit History 69 Commits
__pycache__		__pycache__
analysis		analysis
apps		apps
bin		bin
dockerfile		dockerfile
formats		formats
graphics		graphics
pipeline		pipeline
pyGenomeTracks		pyGenomeTracks
utils		utils
.gitignore		.gitignore
README.md		README.md
__init__.py		__init__.py
__init__.pyc		__init__.pyc
__main__.py		__main__.py
requirement.txt		requirement.txt

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TDGP

Three Dimensional Genome Pipeline

my 3D genome pipeline and scripts

Install

export PATH=/path/to/TDGP/bin:/path/to/TDGP/utils:$PATH
export PYTHONPATH=/path/to/TDGP:$PYTHONPATH

Dependencies

requirement

pysam
cooler
joblib
numpy = 1.16.1
matplotlib
pandas
pyranges
seaborn >= 0.9.0
snakemake
xlwt

optional

pyGenomeTracks
deeptools
tadlib

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my 3D genome pipeline and scripts repository

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Python 94.0%
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Perl 1.3%
R 0.7%
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