intom: Perturbational robustness estimation using integrative omics data

Usage

Using perturbational data directly

intom diff --input-path "inputs/sids.tsv" --output-path "outputs/diff_cli.yaml" --values-path "inputs/freq.tsv" --col-id "t id" --col-group "g id" --cols-value '["freq", "pert"]' --pms-diff '{"func": "ttest"}'
    
⚙️ Processing ..
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🗂️ Saving outputs ..
✅ Done.

intom diff --help

usage: intom diff [-h] [--input-path INPUT_PATH] [--output-path OUTPUT_PATH] [--col-id COL_ID] [--col-group COL_GROUP] [--col-sid COL_SID] [--values-path VALUES_PATH] [--cols-value COLS_VALUE] [-p PMS_DIFF] [-b BU_SCORE_GT] [--kws-scoring KWS_SCORING] [--kws-ro KWS_RO]
                  [--output-dir-path OUTPUT_DIR_PATH] [-t TABLE_EXT] [--verbose VERBOSE] [-r REF_PATH] [--ids-path IDS_PATH] [--mod-cfgs MOD_CFGS] [--mod-names MOD_NAMES] [-s SIDS] [--kws-scoring-flt KWS_SCORING_FLT] [--col-ids-skip-in COL_IDS_SKIP_IN]
                  [--kws-run-tasks-default KWS_RUN_TASKS_DEFAULT]

Differential analysis to robustness probabilities.

Notes:
    See the `intom/examples/inputs` directory for example inputs.
    Use json-string format for the non-string parameters.
    Parameters could be provided using a dictionary file: `--input-path params.yaml`

options:
  -h, --help            show this help message and exit
  --input-path INPUT_PATH
                        -
  --output-path OUTPUT_PATH
                        -
  --col-id COL_ID       -
  --col-group COL_GROUP
                        -
  --col-sid COL_SID     'sample id'
  --values-path VALUES_PATH
                        -
  --cols-value COLS_VALUE
                        -
  -p PMS_DIFF, --pms-diff PMS_DIFF
                        {'col_diffid': None, 'func': 'limma', 'kws_diff': {'robust': True, 'trend': False, 'env_name': None}, 'col_score': 'LFC'}
  -b BU_SCORE_GT, --bu-score-gt BU_SCORE_GT
                        0
  --kws-scoring KWS_SCORING
                        {'value_min': 0.1}
  --kws-ro KWS_RO       {}
  --output-dir-path OUTPUT_DIR_PATH
                        -
  -t TABLE_EXT, --table-ext TABLE_EXT
                        'pqt'
  --verbose VERBOSE     -
  -r REF_PATH, --ref-path REF_PATH
                        -
  --ids-path IDS_PATH   -
  --mod-cfgs MOD_CFGS   -
  --mod-names MOD_NAMES
                        -
  -s SIDS, --sids SIDS  -
  --kws-scoring-flt KWS_SCORING_FLT
                        {}
  --col-ids-skip-in COL_IDS_SKIP_IN
                        'ids'
  --kws-run-tasks-default KWS_RUN_TASKS_DEFAULT
                        {'kernel': 'intom', 'force': False, 'test': False, 'cpus': 1}

(Optional) Pre-processing

intom pair --input-path "inputs/tids.tsv" --output-path "outputs/pair_cli.yaml" --col-id "t id" --col-group "g id" --mod-names '["freq", "pert"]' --values-path "inputs/mods.h5mu" --pairs-path "inputs/tids_sim.tsv" --drop-ids-path "inputs/drop_ids.tsv" --drop-ids-ref-path "inputs/drop_ids_ref.tsv" --kws-pre '{"corr_min": 0.1}'

intom pair --help

usage: intom pair [-h] [--input-path INPUT_PATH] [-o OUTPUT_PATH] [--pairs-path PAIRS_PATH] [-s SIDS] [--drop-ids-path DROP_IDS_PATH] [--drop-ids-ref-path DROP_IDS_REF_PATH] [-v VALUES_PATH] [--mod-names MOD_NAMES] [--mod-cfgs MOD_CFGS] [--idt IDT]
                  [--col-sid COL_SID] [--col-group COL_GROUP] [--col-id COL_ID] [--pms-diff PMS_DIFF] [-b BU_SCORE_GT] [--kws-pre KWS_PRE] [--kws-pair KWS_PAIR] [--kws-scoring KWS_SCORING] [--kws-scoring-flt KWS_SCORING_FLT] [--kws-ro KWS_RO]
                  [--table-ext TABLE_EXT] [-w WD_PATH] [--kernel KERNEL] [--cpus CPUS] [-f] [--test]

(Optional) Pre-processing to pair IDs.

Notes:
    See the `intom/examples/inputs` directory for example inputs.
    Use json-string format for the non-string parameters.
    Parameters could be provided using a dictionary file: `--input-path params.yaml`

options:
  -h, --help            show this help message and exit
  --input-path INPUT_PATH
                        -
  -o OUTPUT_PATH, --output-path OUTPUT_PATH
                        -
  --pairs-path PAIRS_PATH
                        -
  -s SIDS, --sids SIDS  -
  --drop-ids-path DROP_IDS_PATH
                        -
  --drop-ids-ref-path DROP_IDS_REF_PATH
                        -
  -v VALUES_PATH, --values-path VALUES_PATH
                        -
  --mod-names MOD_NAMES
                        -
  --mod-cfgs MOD_CFGS   -
  --idt IDT             -
  --col-sid COL_SID     'sample id'
  --col-group COL_GROUP
                        -
  --col-id COL_ID       -
  --pms-diff PMS_DIFF   {'col_diffid': None, 'func': 'limma', 'kws_diff': {'robust': True, 'trend': False, 'env_name': None}}
  -b BU_SCORE_GT, --bu-score-gt BU_SCORE_GT
                        0
  --kws-pre KWS_PRE     {}
  --kws-pair KWS_PAIR   {}
  --kws-scoring KWS_SCORING
                        {'value_min': 0.1}
  --kws-scoring-flt KWS_SCORING_FLT
                        {}
  --kws-ro KWS_RO       {}
  --table-ext TABLE_EXT
                        'pqt'
  -w WD_PATH, --wd-path WD_PATH
                        -
  --kernel KERNEL       'intom'
  --cpus CPUS           1
  -f, --force           False
  --test                False    

Installation

To use with limma (recommended), refer to setup.sh

cd intom
uv sync
uv pip install .

Citation

@article{dandage_2026a,
title = {Recursive mutational robustness in cancer through intra- and intergenic compensation},
}