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scicone

Description

scicone website

Single-cell copy number calling and event history reconstruction (SCICoNE). A statistical model and MCMC algorithm tailored to single-cell copy number profiling from shallow whole-genome DNA sequencing data. SCICoNE reconstructs the history of copy number events in the tumour and uses these evolutionary relationships to identify the copy number profiles of the individual cells.

Environment Modules

Run module spider scicone to find out what environment modules are available for this application.

Environment Variables

  • HPC_SCICONE_DIR - installation directory
  • HPC_SCICONE_BIN - executable directory

Additional Usage Information

SCICoNE is available on HyPerGator and below is more info regarding the SCICoNE module executables, as well as some info on using custom scripts provided in the SCICoNE Github repository.

SCICoNE CLI Executables

Once SCICoNE is loaded, you will have access to 6 new executables:

  • simulation
  • inference
  • score
  • tests
  • breakpoint_detection
  • save_root_per_nu

These will be available to run anywhere which differs from the official CLI tutorial instructions.

Python usage

Upon loading the SCICoNE module, the scicone package should be available to import into a python script with no problem. But, it is necessary to specify the install path of SCICoNE if creating a SCICoNE object. Make sure to put this as the install path whenever scripting with SCICoNE objects:

  • /apps/scicone/1.0.0/bin/

Example script:

import scicone

install_path = '/apps/scicone/1.0.0/bin/'
temporary_outpath = './'
seed = 42

sci = scicone.SCICoNE(install_path, temporary_outpath, verbose=True)

sim = sci.simulate_data(n_cells=200, n_nodes=5, n_bins=1000, n_regions=40, n_reads=2000, nu=5.0, ploidy=2, s    eed=seed)

More examples and information is avalable at these links below:

The SCICoNE developers also provided some python scripts which are used in their tutorials that you can download and run as well which are available in the SCICoNE github.

Categories

biology, genetics, sequencing, data_science, simulation