MethSCAn 1.1.0 - adds an option to merge VMRs/DMRs that are very close

This release introduces the --bridge-gaps parameter to methscan scan and methscan diff.

By default, methscan scan runs a sliding window along the genome. Overlapping windows exceeding a certain variance threshold are then merged in a peak-calling procedure, yielding VMRs of variable size depending on the width of the variance peak. If there are long stretches of variably methylated DNA, this peak-calling can sometimes produce "fragmented VMRs", i.e. many nearby VMRs that are separated by very small gaps:

In this illustration, many VMRs (thick vertical purple lines) were detected in the gene body of the depicted gene. Since some of these VMRs are only separated by a tiny gap, it may be more appropriate to merge them into one continuous, large VMR.

This VMR merging is now possible by setting --bridge-gaps to e.g. 1000, which would mean that VMRs with a gap of 1000 bp or less will be merged into one VMR, as illustrated here on some mock data:

(red thick line: regular VMR peak calling; blue thick line: VMR peak calling with --bridge-gaps 400. The variance threshold is at 0.55; the y position of the thick lines has no meaning).

The same functionality was also added to the DMR detection approach implemented in methscan diff.

This release also fixes a minor bug in the calculation of the adjusted p-values associated with DMRs.

MethSCAn 1.0.2 - link publication and website; crash on empty bed file

This is a minor release that links our publication and website in the CLI help messages.
Furthermore, MethSCAn now prints an appropriate error message if you provide it with an empty bed file.

MethSCAn 1.0.1 - minor improvements

This is a minor release that adds three tiny features:

1. methscan filter can now filter in place, i.e. overwrite its own input directory with a filtered version of itself
2. methscan scan now aborts properly when no VMRs above the --min-cells threshold are found
3. Added a command to show citation info and a link to our paper.

MethSCAn 1.0.0 - initial release

This is the initial release of MethSCAn upon acceptance of our paper. The main difference is that we renamed the package from scbs to MethSCAn.

For earlier releases and changelogs, check the old repository and its release page.