Changelog • OikScrambling

Updated dN/dS data.

Add nematode comparisons.

A lot of exploratory changes not documented about inversions (sorry), plus:
The Norway TxDB object now has a correct genes() output, and its transcript IDs have an additionnal .t1 suffix.
The calcOperons function now ignores nested genes, as they do not interrupt collinearity.
These changes require the package to be reloaded, but the 4.0.0 RData object can still be used.

Reformed the wgo object to match the 4 classes: isolated alignment, breakpoint region, collinear alignment and bridge region.

Alignment features plotted on operon boundaries for Figure 3.
New chromosome plots for Figure 4.
New panel showing that short bridge regions are mostly made of short introns.

Explore strand proportion indices.
New region width plots for Figure 2.

Draft chromosome plots for Figure 4 (ex-3, ex-2b).
Natural scale width plots for Figure 2
5-panel feature plots for Figure 2

Mid-centered feature plots for Figure 2.

Plot genomic features on white background for Figure 2.
Compute strand randomisation indexes.
Provide alignment information for manual brush-up of Hox panels in Figure 1.
Add Osaka–Aomori Oxford plots.

Plot operons density near alignment boundaries.
Compute confidence intervals on width distributions.
Plot width distributions in PDF format.

Corrected arm names on query genomes.
New functions isSyntenic(), isSynbrachial(), nameSyntenic() and nameSynbrachial().
Renamed mapped unaligned regions to bridge regions and renamed unalMap object to bri.
Added an ‘isolated’ category in the RegionWidths vignette.

Parallel plot of chr2
Export aggregated numbers about segment widths.

New Oki-Osa Oxford plots for Figure 1.

Strand-colored version of the 10-Mb window Oxford plots. Needs GenomicBreaks version 0.13.1 or superior.
Human-mouse 10-Mb window Oxford plot. Needs BreakpointsData version 3.9.0 or superior.

Add a vignette about the movement of the PAC3 gene.

Adopt semantic versionning: any backwards-incompatible change increases the major version number, no matter how (un)important it is.
Use the new GenomicBreaks::bridgeRegions() function that produces zero-width ranges instead of the local function that artificially added 1nt to the ends.

Major change in the BSgenome packages, needing the removal of the old ones and the recomputation of the data. The new packages allow to much easier link the GBreaks objects to their genome sequence or annotations.

Move some regions of interest in a separate vignette.

Added a new SegmentMovements vignette.

Added a new wgo whole-genome object indicating if a base is part of a syntenic block, or just aligned, or unaligned.

Added nonCoa flags to the gbs, unal and coa objects.

Created compound plots of width distribution for Figure 2.

Overlap with repeats on both strands. The difference is not so massive, considering that the unaligned and unmapped regions are already strandless anyway.

New functions OikScrambling:::compDistClass() and OikScrambling:::compDistClass(), and new option short for OikScrambling:::compDistance(), to produce more compact summary graphs.

Identify the flipped repeat as MITE and search for other copies.

Add regions of interest with repeat flipping and insertion.

Add Hox regions of interest for Figure 1

Add 10-Mbp dot plots for Figure 1

Add Mike’s vignette on coalescing cutoffs.

Adding Drosophila data for a plot on CP’s MBSJ2021 poster.

load_one_to_ones() function moved from GenomicBreaks to this package.
Internal functions updated to load C. intestinalis annotations.

From now on the main branch must remain buildable.
Added a NEWS.md file to track changes to the package.