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TODO.md

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Primary

  • Fix networkDiffusion to keep dimnames.
  • Fix broken R functions
  • Edit the package 'DESCRIPTION'.
  • Edit the exports in 'NAMESPACE', and add necessary imports.
  • Consolidate decompACTION and runACTION
  • Add rerun archetype merging
  • Separation ACTION and ACTIONet
  • Creature "run pipeline" function
  • Fix plotting
  • interactive 3D coords
  • Generalize "correctBatchEffect" for matrix input after fixing back-end
  • Incorporate bact ortho into reduceKernel (requires generalized reduceKernel)
  • Replace plot.marker.enrichment.by.archetype.heatmap and plot.marker.enrichment.by.cluster.heatmap
  • Change coordinate ionitialization to "archetype_footprint" in runACTIONet()
  • In plot.ACTIONet(), plotting order should have NA points on bottom.
  • Fix bug in plot.ACTIONet() and .layout_plot_labels() when label_attr contains empty string ("")
  • Finish annotateClusters
  • Add error for annotateClusters for when feat_spec is not in object.
  • Force all zero rows removed if min_cells_per_feat > 0 in filter.ace
  • Fix impute with single gene

Secondary

  • Change ggtheme to bw
  • Add arbitrary pseudo count
  • Normalize only subset of features

Done

  • New marker detection
  • WOrking and improved ledien via igraph
  • New qc functions
  • Removed C_fastSpMatViewSum due to inaccuracy when multithreading.