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Releases: MoTrPAC/MotrpacRatTraining6mo

Try try again

06 Jan 23:11
30c53e7
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Summary

  • In plot_feature_normalized_data() and plot_feature_logfc(), handle input features that don't exist in the data.

What's Changed

Full Changelog: v1.4.2...v1.4.3

Happy plotting

06 Jan 22:24
41beee7
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Summary

  • Dodge points in plot_feature_normalized_data() and plot_feature_logfc() for readability.
  • Make plot_feature_normalized_data() and plot_feature_logfc() more accommodating of features with multiple measurements.
  • Add add_adj_p parameter to plot_feature_normalized_data().
  • Add return_data parameter to plot_feature_logfc().
  • Return NULL instead of error if data doesn't exist for plotting plot_feature_normalized_data() in loops.

What's Changed

Full Changelog: v1.4.1...v1.4.2

Ladybug

06 Jan 18:01
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Summary

  • Fix custom_cluster_pathway_enrichment() to accept a list of lists as input.
  • Use filtered feature-to-gene map to perform pathway enrichment.
  • In cluster_pathway_enrichment(), remove pathway enrichments driven by a single gene
    for consistency with the landscape paper.

What's Changed

Full Changelog: v1.4.0...v1.4.1

Party gene

05 Jan 16:57
8fe4d62
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Summary

  • Add gene_pathway_enrichment() (wrapper for gprofiler2::gost()).
  • Add example to "Get Started" vignette.

What's Changed

Full Changelog: v1.3.0...v1.4.0

Workshop ready

05 Jan 03:08
09cf9d9
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Summary

  • Add df_to_numeric() to easily format data frames.
  • Add plot_feature_normalized_data() to plot normalized sample-level data for a single feature.
  • Add plot_feature_logfc() to plot differential analysis results for a single feature.
  • Add more examples and screenshots to the "Get Started" vignette.

What's Changed

Full Changelog: v1.2.0...v1.3.0

Tis the season

28 Dec 02:33
2e93f3c
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Summary

  • Add functions to perform meta-analysis and meta-regression of redundant metabolites.
  • Add load_training_da() to load training summary statistics from GSC.
  • Retain order of input vial labels in result of viallabel_to_pid().

What's Changed

Full Changelog: v1.1.0...v1.2.0

Attack outliers

10 Oct 22:34
a8ce073
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Summary

  • Add atac_call_outliers()
  • Bug fix in atac_prep_data()

What's Changed

Full Changelog: v1.0.2...v1.1.0

Zoomies

08 Oct 22:49
2ed2605
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Summary

  • Use a hashmap to speed up calculation of similarity scores in enrichment_network_viz() (thanks, Jay Yu)
  • Improve visInteraction settings in enrichment_network_viz(), i.e., show edges on zoom and slow down zoom
  • Don't run memory-intensive examples and vignette code blocks to prevent GitHub Actions OOM error

What's Changed

Full Changelog: v1.0.1...v1.0.2

I spoke too soon

22 Sep 00:16
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Summary

Fix bugs:

  • missing : in transcript_timewise_da()
  • counts improperly filtered in transcript_prep_data()
  • DESeq2 prefix missing from counts() in transcript_timewise_da()

Dev:

  • keep examples from printing too much output
  • rename tutorial.Rmd to MotrpacRatTraining6mo to take advantage of "Get Started" pkgdown feature
  • add @keywords internal to functions that are not exported to prevent them from showing up in site index

What's Changed

Full Changelog: v1.0.0...v1.0.1

Let's get some traffic!

20 Sep 20:42
bf1e1cb
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Summary

What's Changed

Full Changelog: https://github.com/MoTrPAC/MotrpacRatTraining6mo/commits/v1.0.0