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Supplemental Information

Supplementary Data containing Supplementary Figures and Tables

DOI: 10.7287/peerj.preprints.2585v1/supp-1

Text reporting results from the simulations performed to evaluate method performance and an investigation of the power of the method

DOI: 10.7287/peerj.preprints.2585v1/supp-2

Text outlining more details of the analyses using pathVar on human ESC and iPSC data sets

DOI: 10.7287/peerj.preprints.2585v1/supp-3

Text outlining more details on the analyses performed on other data sets used to evaluate the pathVar method

DOI: 10.7287/peerj.preprints.2585v1/supp-4

Raw code for functions used in the pathVar method

DOI: 10.7287/peerj.preprints.2585v1/supp-5

Raw code for class definitions used in pathVar package

DOI: 10.7287/peerj.preprints.2585v1/supp-6

A zip file containing the raw code files used to generate results in this manuscript

Files have been organized into the folders corresponding to the analyses represented in the Results sections of the manuscript.

DOI: 10.7287/peerj.preprints.2585v1/supp-7

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Laurence de Torrente conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Samuel Zimmerman performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Deanne Taylor reviewed drafts of the paper, provided feedback that improved the method during its development..

Yu Hasegawa analyzed the data, prepared figures and/or tables.

Christine A Wells reviewed drafts of the paper, provided feedback that improved the method during its development..

Jessica C Mar conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Data Deposition

The following information was supplied regarding data availability:

The manuscript describes a computational method that is publically available via Bioconductor. As a requirement for acceptance into Bioconductor, we had to supply a vignette outlining code that demonstrates how the method works on data. This code is included in the vignette. The raw code is available on email request. However, if useful - we can also deposit the raw code of the actual method into a GitHub repository that our lab has.

Funding

S.Z and J.C.M were supported by the New York State Department of Health (NYSTEM Program) shared facility grant (C029154). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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