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Dip-C v1.0.0

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@conchoecia conchoecia released this 04 Mar 08:09
v1.0.0
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Dip-C v1.0

This is the first versioned release of the dip-c software, marking the stable version of the software that has been used in the following publications:

  • Tan, Longzhi*; Xing, Dong*; Chang, Chi-Han; Li, Heng; Xie, X. Sunney "Three-dimensional genome structures of single diploid human cells," Science 43, 924-928. DOI:10.1126/science.aat5641 (2018)
  • Tan, Longzhi*; Xing, Dong*; Daley, Nicholas; Xie, X. Sunney "Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems," Nature Structural & Molecular Biology 26, 297-307. DOI:10.1038/s41594-019-0205-2 (2019).
  • Tan, Longzhi†; Ma, Wenping; Wu, Honggui; Zheng, Yinghui; Xing, Dong; Chen, Ritchie; Li, Xiang; Daley, Nicholas; Deisseroth, Karl; Xie, X. Sunney† "Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development," Cell 184, 1-18. DOI:10.1016/j.cell.2020.12.032 (2021).
  • Tan, Longzhi*†; Shi, Jenny*; Moghadami, Siavash; Parasar, Bibudha; Wright, Cydney P.; Seo, Yunji; Vallejo, Kristen; Cobos, Inma; Duncan, Laramie; Chen, Ritchie; Deisseroth, Karl† "Lifelong restructuring of 3D genome architecture in cerebellar granule cells," Science 381, 1112-1119. DOI:10.1126/science.adh3253 (2023).

About this release

Dip-C v1.0 represents the Python 2 codebase as used in the above publications.
This release is provided for reproducibility and archival purposes.

What's included

  • Core Dip-C commands for:single-cell diploid 3D genome reconstruction: segment extraction, contact extraction, haplotype imputation, 3D structure analysis, and visualization.
  • Precomputed color files for hg19, hg38, and mm10 reference genomes
  • Conversion scripts for integration with hickit, Juicer Tools, and other formats
  • Patches for nuc_dynamics (legacy standalone workflow)

Requirements

  • Python 2.7+ with NumPy and SciPy
  • pysam (for BAM file processing)
  • External tools for full workflows:
    • BWA
    • SAMtools
    • hickit
    • PDBx Python Parser
    • PyMol
    • rmsd (Python package)

See the README for detailed requirements and usage instructions.

Installation

Clone the repository and add it to your PATH:

git clone https://github.com/tanlongzhi/dip-c.git
export PATH=$PATH:$(pwd)/dip-c

Looking ahead

Development will shift to a Python 3 version of Dip-C, which will also be published on PyPI and conda for easier installation. This v1.0 release preserves the original Python 2 codebase as a reference.

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