Dip-C

Diploid Chromatin Conformation Capture — reconstruct 3D diploid genomes from single cells.

Installation

Recommended installation (conda + pip)

The easiest way to ensure that the installation will work on your system, regardless of the age of its software, is to create a conda environment and pre-install the compiled dependencies, then install Dip-C with pip:

conda create -n dipc python=3.11
conda activate dipc
conda install -c conda-forge -c bioconda numpy scipy pysam
pip install run-dipc

Note: If you see Run 'conda init' before 'conda activate' (common on HPC clusters), run this first:

source $(conda info --base)/etc/profile.d/conda.sh

Verify the installation:

dip-c --help

Alternative: pip-only install

On modern systems (macOS, Ubuntu 20.04+, RHEL 8+), pip can install everything directly. This is worth trying, but if it fails for any reason we suggest using the above conda + pip installation method:

pip install run-dipc

Why does pip fail on older Linux? (optional reading): If pip failed, use the conda + pip method above. Older systems like CentOS/RHEL 7 have an old C library (glibc < 2.28), so prebuilt packages for NumPy, SciPy, and pysam are not available. Pip falls back to compiling them from source, which takes 15–30 minutes and requires a C++17-capable compiler. If that build also fails with C++ Compiler does not support -std=c++17, the system's C++ compiler is too old. You can install a newer one with:

conda install -c conda-forge gcc_linux-64 gxx_linux-64

But the simplest path is to skip all of this and use the recommended conda + pip installation above.

Upgrading

If you already have Dip-C installed and want to update to the latest version:

pip install --upgrade run-dipc

Usage

dip-c <command> [options]

Run dip-c with no arguments to see all available commands.

Documentation

Full documentation, workflows, and file format specifications are available on GitHub:

https://github.com/tanlongzhi/dip-c

Citations

Please cite the original Dip-C paper:

Tan, Longzhi*; Xing, Dong*; Chang, Chi-Han; Li, Heng; Xie, X. Sunney "Three-dimensional genome structures of single diploid human cells," Science 361, 924-928 (2018). DOI:10.1126/science.aat5641

License

MIT