Dependencies

• fairscape-cli

• scipy

• scikit-learn

• pandas

• numpy

• dill

Compatibility

• Python 3.8+

Installation

git clone https://github.com/idekerlab/cellmaps_utils
cd cellmaps_utils
make dist
pip install dist/cellmaps_utils*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages

Before running tests, please install pip install -r requirements_dev.txt

For developers

# From base directory of this repo cellmaps_hierarchyeval
pip uninstall cellmaps_utils -y ; make clean dist; pip install dist/cellmaps_utils*whl

Cite

If you find this tool useful, please cite:

Lenkiewicz, J., Churas, C., Hu, M., Qian, G., Jain, M., Levinson, M. A., … & Schaffer, L. V. (2025). Cell Mapping Toolkit: An end-to-end pipeline for mapping subcellular organization. Bioinformatics, 41(6), btaf205.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template

0.10.0 (2026-10-12)

• Added --input_format zmadex_saint to cellmaps_utilscmd.py apmsconverter which consumes the Zmadex/SAINT AP-MS analysis and writes a normalized apms.tsv. The legacy input format is unchanged and remains the default

• apmsconverter now writes apms_unfiltered.tsv with the complete pre-filter matrix alongside the filtered apms.tsv, controlled by --filter and --no_unfiltered

• apmsconverter now accepts --drug_effect_input holding MSstats drug effect results, published as a separate apms_drug_effect.tsv so apms.tsv keeps the same schema in every RO-Crate. Row selection is controlled by --drug_effect_rows

• apmsconverter now writes apms_qc.json summarizing row counts, join coverage and gene set membership

• Added cellmaps_utilscmd.py secmsconverter to package Spectronaut SEC-MS TSV exports into a RO-Crate. --inputs accepts file/replicate pairs, copied as secms_<replicate>.tsv with quantities and missing values preserved and without averaging replicates

• secmsconverter writes dataset metadata, including replicate labels, to data_info.json, registers datasets, software and computation provenance, and includes a SEC-MS readme.txt describing the data and column labels

• Added SEC-MS conversion documentation and updated RO-Crate release tables to classify SEC-MS crates as data

0.9.0 (2025-07-03)

• Add statistics generator for ro-crates

• Fix provenance bugs for new versions of ro-crate

0.8.0 (2025-04-23)

• Set maximum supported version of scipy to <1.11

• Added tworeplchallenge and solution_generator commands to cellmaps_utilscmd.py. These commands generate a Kaggle challenge and solution from a SEC-MS dataset

• Updated to PEP 517 compliant build system

0.7.0 (2025-03-05)

• Add compute_hierarchy_robustness method to HierarchyDiff class to assess the robustness of a hierarchy based on Jaccard similarity across multiple alternative hierarchies.

0.6.0 (2025-02-05)

• Add HierarchyDiff class with compare_hierarchies method to compare two hierarchies in CX2 format, and output a hierarchy with robustness score of each system.

• Add version bounds for required packages.

• Add convert_hierarchical_network_to_hcx (utility function that aids convertion of a hierarchical network in CX2 to HCX) and add_hcx_members_annotation (adds ‘HCX::members’ attribute to nodes) to hcx_utils

• Fixes in IF and APMS tools

0.5.0 (2024-09-05)

• Add HiDeFToHierarchyConverter, a class to convert a edge list and node list in HiDeF format to hierarchy in HCX.

• Add InteractomeToDDOTConverter and DDOTToInteractomeConverter, classes to convert network in CX2 format to DDOT format and vice versa, HierarchyToDDOTConverter and DDOTToHierarchyConverter, classes to convert hierarchy network in HCX format to DDOT and vice versa.

0.4.0 (2024-07-02)

• Updated provenance utils, added checks in for missing data in input RO-Crate, and allowing to continue but logging errors in the process

• Add HierarchyToHiDeFConverter, a class to convert a hierarchy network (in CX2 format) to a HiDeF format nodes and edges lists.

• Add NDExHierarchyUploader, a class for uploading hierarchy and its parent network to NDEx.

• Updated cellmaps_utilscmd.py apmsconverter, ifconverter, crisprconverter to support tissue as well as output data_info.json file to resulting RO-Crate so subsequent tools can more easily get provenance information

• Updated cellmaps_utilscmd.py crisprconverter to consume .h5ad files and updated readme.txt file

0.3.0 (2024-04-15)

• Bumped fairscape-cli dependency to 0.2.0

0.2.0 (2024-02-20)

• Bumped fairscape-cli dependency to 0.1.14 to support schemas

• Added support for schema to data_dict parameter in ProvenanceUtil.register_dataset()

• Added --release flag to cellmaps_utilscmd.py rocratetable and in output table renamed “Name of Computation” to “Name” as well as added “Type”, “Cell Line”, “Treatment”, “Gene set”, and “Version” to table output

• Set default logging level to ERROR for cellmaps_utilscmd.py command

0.1.0 (2024-01-01)

• First release on PyPI.