janusbio 0.3.0

JANUS: Joint ANalysis for augmentation of clUSter specificity

JANUS CLI

This project can be run from the command line with janus.py or python -m janusbio.cli.

Input format

• Provide 2 raw datasets:
  • --ref: reference dataset
  • --exp: experiment dataset
• Expected format for both files:
  • genes as rows
  • samples as columns
• Supported file types:
  • .csv
  • .xlsx
  • .parquet
  • .p

Do not pass precomputed contribution or correlation matrices.

Basic usage

Run one or more formulas from the command line:

python janus.py \
  --ref depmap_23Q2_chronos.csv \
  --exp mito_screens.csv \
  --pairwise_contribution \
  --get_covariation_contributions \
  --get_differential_correlation

Equivalent module form:

python -m janusbio.cli \
  --ref depmap_23Q2_chronos.csv \
  --exp mito_screens.csv \
  --pairwise_contribution

Available flags

Required inputs

• --ref <path>: path to the reference dataset
• --exp <path>: path to the experiment dataset

Formula selection

• --pairwise_contribution

  • runs get_contributions(...)
  • produces reference and experiment contribution matrices

• --get_covariation_contributions

  • runs get_covariation_contributions(...)
  • produces reference and experiment covariation contribution matrices

• --get_differential_correlation

  • runs get_differential_correlation(...)
  • produces differential-correlation and direction matrices

At least one formula flag must be provided.

Optional output

• --output <directory>
  • if provided, results are saved as parquet files

Example:

python janus.py \
  --ref depmap_23Q2_chronos.csv \
  --exp mito_screens.csv \
  --pairwise_contribution \
  --get_covariation_contributions \
  --get_differential_correlation \
  --output output

Output files

Depending on the selected flags, the CLI writes:

• pairwise_reference_contribution.parquet
• pairwise_experiment_contribution.parquet
• covariation_reference_contribution.parquet
• covariation_experiment_contribution.parquet
• differential_correlation.parquet
• differential_correlation_direction.parquet

Help

To see CLI help:

python janus.py --help

Or:

python -m janusbio.cli --help