NEWS

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damidBind 1.1.1

• NEW: Added additional diagnostic plots (mostly used to generate supplementary figures in the damidBind manuscript): plot_catada_mean_variance() and test_weighting_vs_bias_artifact()
• NEW: load_data_peaks() and load_data_genes() now support multiple normalisation options: quantile normalisation ("quantile"), cyclic LOESS norm ("loess"), and RPM (reads per million) norm ("rpm". The default is "none" (no normalisation).
• NEW: a pre_scale option has been added to both load_data_peaks() and load_data_genes(), which will perform zero-preserving (uncentred) scaling (via base R scale(center=FALSE, scale=TRUE)) prior to normalisation. The default is FALSE.
• NEW: all input metadata and genome annotation metadata are saved in the DamIDResults S4 object. Basic metadata are displayed with the default show() method, and all are accessible via the metadata() accessor.
• NEW: plot_volcano() now takes a new labels option, values of "all", "highlight", or a character vector containing one or more group names from the highlight list. Only this group will be labelled on the plot. The original label configuration options still remain.
• NEW: plot_volcano() supports highlight groups of either loci or gene names, including different categories in the same plot. The default "auto" behaviour matches a highlight group against whichever definition has the most matches, but use the new highlight_by option to enforce matching by either "gene_name" or "id" (i.e. locus).
• CHANGED: deprecated the quantile_norm option for load_data_peaks() and load_data_genes().
• Added a citation to the current bioRxiv preprint on damidBind

damidBind 1.0.0

• damidBind was automatically bumped to version 1.0.0 via Biocondutor release 3.23.

damidBind 0.99.14

• NEW: Added average_tracks option to browse_igv_regions(). When TRUE, this feature displays averaged binding tracks per condition rather than replicates.
• NEW: Added export_data_archive option to browse_igv_regions(). When set to a valid file path, this parameter will export the tracks that would be displayed in the Shiny IGV window as bedGraph or BED files in a zip archive, instead of launching the Shiny app. These files can be used to render final publication figures via external utilities such as pyGenomeTracks if desired. This option can of course be combined with average_tracks above.

damidBind 0.99.12

• CHANGED: major rewrite of the occupancy FDR logic for gene expression status. Briefly:
  • Model regression fits have been improved with weighted natural spline fits for Tier 2 regressions (relationship is not log-linear)
  • Threshold scores for null model fitting are now determined from input data
  • Diagnostic plots for Tier 2 regressions have been added
  • Empirical p-values now aggregated on a condition level by default, using either Stouffer's (default) or Fisher's method
  • Occupancy p-values are now calculated by default during data loading, and merged during differential_binding(), before BH adjustment is applied to the aggregated p-values per condition. See the relevant man pages for more details.
• CHANGED: internal logic for handling condition names and matches
• FIXED: Venn diagram universe logic now correctly determines the expressed gene universe when handling RNA Polymerase datasets

damidBind 0.99.10

• NEW: plot diagnostics for sample loading (PCA, clustered correlation heatmap)
• NEW: plot diagnostics for limma functions (eBayes moderation / SA plots)
• NEW: limma functions now use trend and robust by default to better fit heteroscedastic DamID data
• NEW: new function extract_unique_sample_ids generates simplifed, unique sample names from complex filenames for display (in diagnostic plots, IGV/Shiny browser)
• CHANGED: dense point labelling function now uses exact dbscan kNN functions, not approximate HNSW functions
• CHANGED: differential threshold filtering can now be set to non-zero values
• CHANGED: default replicate filtering for differential analyses is set to the minimum number of the two condition replicates

damidBind 0.99.9

• FIXED: igvShiny code now correctly handles the new internal GRanges binding profile data objects

damidBind 0.99.8

• Unicode removed from documentation to allow latex generation :/

damidBind 0.99.6

• NEW: Differential analyses now optionally screen out loci with negative signal in a specified number of replicates per sample (default is 2). These loci are removed before differential analysis.
• NEW: Geneset universe calculations now take into account the low-signal screening; universe is determined only on the loci passing filter.
• NEW: Loci labels are optionally sampled to allow labels even in highly-dense plot regions. Sampling algorithm determines a KNN graph from points, then uses this to select only a subset of total labelled points. A default parameter is provided, but all algorithm parameters are fully customisable.
• NEW: Test conditions specified via the cond parameter can now use regexes, when regex = TRUE is set.
• CHANGED: Test conditions specified via cond now use a simple named vector, merging cond and cond_names.
• CHANGED: Improved and fixed underlying logic and tests to handle the cond parameter change
• CHANGED: Substantially improved legend guide handling parameters and logic for volcano plots
• FIXED: a number of minor bugfixes, code refactoring and tidying.

damidBind 0.99.4

• NEW: Added in FDR modelling and calculation routines for RNA Polymerase occupancy
• NEW: plot_volcano and plot_venn functions can now filter for FDR when plotting
• NEW: expressed() accessor method for obtaining all genes passing an FDR threshold for a specific condition
• CHANGED: binding profile data is now stored as a GRanges object
• CHANGED: analyse_go_terms now returns the clusterProfiler results object for downstream use
• Begun incorporating gseGO functionality into analyse_go_terms
• Improved documentation of DamIDResults class and accessors
• Added more details to the package vignette
• Many small bug fixes

damidBind 0.99.2

• NEW: Added button in IGV viewer to save SVG (useful when viewing window is horizontally compressed and button in the IGV interface is not displayed)
• NEW: New legend customisation options for volcano plots (including a legend internal to the plot frame, now default)
• NEW: More GO term plot customisation options
• FIXED: All volcano plot point labels are now rendered as a single geom layer, preventing ugly overlaps
• Substantial internal refactoring
• Many small bug fixes
• Updated unit tests

damidBind 0.99.0

• Initial submission to Bioconductor.