V0.2.0

What's Changed

• Update peptide_significance_map and plot_peptide_position by @TylerSagendorf in #29
• Major updates to PeCorA functions by @TylerSagendorf in #31
• Rename pecora_msnset to brain_msnset by @TylerSagendorf in #32
• Update ComBat_NA.R by @CamiloPosso in #33
• Dev.parallel fix by @Ben-Drucker in #35
• backtick names() issue fix by @vladpetyuk in #39
• added turbo.colors new color scheme by @vladpetyuk in #42
• addressing issue #43 by @vladpetyuk in #44
• Update PeCorA Code by @TylerSagendorf in #45
• Update function error handling by @TylerSagendorf in #52
• Fix R CMD check core limit error on Mac by @TylerSagendorf in #55
• Added a check to correct_batch_effect_NA by @CamiloPosso in #53
• fix rownames compatibility between exprs and fData by @vladpetyuk in #57
• adding confidence interval to AUC plot by @vladpetyuk in #59
• ggplot version of plotAUC (checked out from ben-reproducibility) by @Ben-Drucker in #61
• init ptm_significance_map by @skelly001 in #63
• Update column names by @skelly001 in #51
• Reproducibility by @Ben-Drucker in #37
• fix seed argument and enable CI toggle by @skelly001 in #66
• remove "Random Model" from legend by @skelly001 in #68
• New plotting function, vignette, and clean up (dev.Ben branch) by @Ben-Drucker in #72
• Develop damon by @vladpetyuk in #75
• Added more algorithms to rrollup by @Ben-Drucker in #76
• added number of PTMs sites into the feature name in multisite type of… by @vladpetyuk in #79
• filtering out of multisites with not all sites localized by @vladpetyuk in #80

New Contributors

• @Ben-Drucker made their first contribution in #35
• @vladpetyuk made their first contribution in #39
• @skelly001 made their first contribution in #63

Full Changelog: v0.1.0...V0.2.0

v0.1.0

Changes since December 27, 2021:

• Added complex_heatmap function to more easily create annotated expression and correlation heatmaps from MSnSet objects. This is a wrapper around functions from the ComplexHeatmap package.
• Added vignette for complex_heatmap.
• Removed plot_sample_correlation_heatmap and plot_sample_correlation_pheatmap. Functionality has been absorbed by complex_heatmap.
• Added plot_upset function to create labeled UpSet plots. This is a wrapper around functions from the ComplexHeatmap package.
• Updated limma_contrasts to add the option to specify which test statistic to report (moderated t or F). Also add multi-dimensional scaling (MDS) plot to new limma_diagnostics helper function (not exported).
• Removed row names from output of msnset2txt.