0.0.0

[gfudenberg]

TODO

• migrate code to download data elsewhere in cooltools (e.g. lib.io)

Notebooks:

i/o

• io #6

pairtools-walkthrough:

• map
• parse
• sort
• dedup
• stats
• discussion of artefacts?..
• cooler aggregation, balancing, zoomify

viz:

• higlass integration
• examples of translocations, other organisms (yeast)
• 45° rotated heatmap plotting (see insulation notebook)
• sample_cooler() ?

contacts_vs_distance:

• trans expected: modify example HFF cooler to have 3 chrms
• save to file

compartments_and_saddles

• saddle.saddleplot, saddle.saddle_strength
• need to re-work to put the discussion of digitization after the simple example, since that is now hidden from the user
  • TBD: download fasta in ipynb or provide pre-binned GC content?
• add examples of saddles for: quantifying GC content preferences, Rabl conformation, etc. #21

insulation_and_boundaries

• Compute insulation, find peaks, visualize w/ map
• pileup/stackup of CTCF ChIP-Seq coverage at boundaries
• boundary filtering, thresholding based on CTCF

pileup_CTCF_boundaries

• everything! (On-diagonal pileups at CTCF ChIP and called boundaries, ..)
• on-diagonal pileups at CTCF peaks
• off-diagonal pileups between CTCF peaks
• adaptive coarsegrain adaptation for pileups ?
• average Rabl configuration ?

dots_and_apa:

• everything! (Dot calling, visualize w/ map, aggregate pileups, pair of CTCF pileups)

also see open2c/cooltools#312

[gfudenberg]

the viz notebook should print the c.bins()[:3] somewhere at the start of the balancing section, and then say aha the weights column is present, this cooler has been balanced
done

[gfudenberg]

added viz notebook should also show an unbalanced matrix in the balancing section, otherwise its not very clear why balancing is relevant.

Q: should this link to cooler-binder (https://github.com/open2c/cooler-binder/blob/master/cooler_api.ipynb), or is that deprecated cc @nvictus ?

[gfudenberg]

maybe good to plot an observed/expected contact map in either contacts_vs_distance, viz, or compartments_saddles?