Response to Reviewers

We received three reviews for this paper, which required additional analyses, clarifying text in figures, and paper restructuring. This release captures all these changes.

What's Changed

• [Response to Review] Add PCA supplementary figure by @gwaygenomics in #54
• [Response to Review] Coefficient of variation supplementary figure by @gwaygenomics in #55
• [Response to Review] Adding dose independent null distribution comparisons by @gwaygenomics in #56
• [Response to Review] Discretize panels in figure 1 and sup fig 3 by @gwaygenomics in #57
• [Response to Review] Adding example distributions: Cell Painting Images and L1000 by @gwaygenomics in #58
• [Response to Review] Add target and pathway labels for prediction by @gwaygenomics in #59
• [Response to Review] Update MOA labels in UMAP visualization by @gwaygenomics in #61
• [Response to Review] Adding precision analysis for MOAs and Targets by @gwaygenomics in #62
• [Response to Review] Comparing cell count, reproducibility, and cell death predictions by @gwaygenomics in #63
• [Response to Review] Adding visualization of MOAs that are not captured by either assay by @gwaygenomics in #64
• [Response to Review] Edge well filter QC percent strong by @gwaygenomics in #65
• [Response to Review] Update figures to clarify Spearman and add percent replicating explainer by @gwaygenomics in #66
• [Response to Review] Filter GO terms for ML analysis by @gwaygenomics in #67
• [Response to Review] Add dose-independent percent matching and average precision experiments by @gwaygenomics in #68
• [Response to Review] Adding MOA matching column to figure 2 with same compounds by @gwaygenomics in #69
• [Response to Reviewers] Update supplementary tables by @gwaygenomics in #70
• Do not track all csv files via git lfs by @gwaygenomics in #71
• [Response to Review] Equal weighting ensemble by @gwaygenomics in #72
• [Response to Reviewers] Update Figure 4F - ORA GO term display by @gwaygenomics in #73
• [Response to Review] Update Figure 5 (Deep learning analysis) by @gwaygenomics in #74
• [Response to Reviewers] Update all figure names by @gwaygenomics in #75

Full Changelog: v1...v2

Paper submission DOI

The same repository state as https://github.com/broadinstitute/lincs-profiling-complementarity/releases/tag/v1 but added to mint Zenodo DOI

Paper submission

All code, data, instructions, results, and figures required to reproduce the analysis for the paper titled: "Morphology and gene expression profiling provide complementary information for mapping cell state"

A companion repository that includes instructions on how to process the LINCS Cell Painting data is located here: https://github.com/broadinstitute/lincs-cell-painting