A light-weight tool for finding Group-, Individual-sample Specific TADs (GISTA) GISTA is composed of three steps: 1). Partitioning the whole genome into a series of TADs arrays across all samples; 2). Constructing a feature vector for each TADs array; 3). Annotating the type of TAD change to each TADs arrays and statistical inference.

WorkFlow

Installation

Step1: install mamba from https://mamba.readthedocs.io/en/latest/installation/mamba-installation.html
Step2: mamba create -n gista python pandas numpy seaborn scipy tqdm logomaker click openpyxl xlsxwriter natsort
Step3: mamba activate gista
Step4: cd <path to the GISTA>
Step5: pip install --editable .

Quick Start

Currently GISTA only accept TopDom output formats (please check the exmaple data). If you need help, please reach out ot me :)

Multi-Samples Mode

# 'RT,PT;PT-RT,NT' mean process RT.vs.PT and PT+RT.vs.NT
# The comparison separate by ';' and treat and control separate by ',',The second sample is control
# see SampleList_Multi.xlsx exmaple in data
GISTA multi -sf SampleList_Multi.xlsx -c 'RT,PT;PT-RT,NT' --binsize 40000

Two-Samples Mode

# 'RT,PT;PT-RT,NT' mean process RT.vs.PT and PT+RT.vs.NT
# The comparison separate by ';' and treat and control separate by ',',The second sample is control
# see SampleList_Multi.xlsx exmaple in data
GISTA two -sf SampleList_Two.xlsx -c 'RT,PT;PT-RT,NT' --binsize 40000

Manual

Please use 'GISTA multi --help' or 'GISTA two --help' to check detailed instruction

Welcome to use GISTA :)
Usage: GISTA [OPTIONS] COMMAND [ARGS]...

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  multi  Multi-samples mode for GISTA
  two    Two-samples mode for GISTA

Multi

Usage: GISTA multi [OPTIONS]

  Multi-samples mode for GISTA

Options:
  -sf, --samplesfile PATH     sample metadata sheet, contain TopDom (like)
                              files, .csv or .xlsx  [required]
  -c, --comparison TEXT       Comparison string in the format 'RT,PT;PT-
                              RT,NT', The comparison separate by ';' and treat
                              and control separate by ',',The second sample is
                              control  [required]
  -bs, --binsize INTEGER      resolution/binsize of the TADs
  -gc, --groupcut FLOAT       Group level high variation cutoff
  -ic, --individualcut FLOAT  Individual level high variation cutoff
  -od, --outdir PATH          Output folder
  --help                      Show this message and exit.

Two

Usage: GISTA two [OPTIONS]

  Two-samples mode for GISTA

Options:
  -sf, --samplesfile PATH     sample metadata sheet, contain TopDom (like)
                              file, .csv or .xlsx  [required]
  -c, --comparison TEXT       Comparison string in the format 'RT,PT;PT-
                              RT,NT', The comparison separate by ';' and treat
                              and control separate by ',',The second sample is
                              control  [required]
  -bs, --binsize INTEGER      resolution/binsize of the TADs
  -gc, --groupcut FLOAT       Group level high variation cutoff
  -ic, --individualcut FLOAT  Individual level high variation cutoff
  -pr, --pseudorep INTEGER    The number of Pseudo-replication
  -od, --outdir PATH          Output folder
  --help                      Show this message and exit.

Citation

If you find this tool useful, please consider cite. Thank you!

Choppavarapu, L., Fang, K., Liu, T., Ohihoin, A. G., & Jin, V. X. (2025). Hi-C profiling in tissues reveals 3D chromatin-regulated breast tumor heterogeneity informing a looping-mediated therapeutic avenue. Cell reports, 44(4).